Publications by BOINC Projects

Our intent is to list papers containing scientific results arising, directly or indirectly, from BOINC-based computing. Please report any issues here.


Group by project · year


ABC@home
AQUA@home
Asteroids@home
Big and Ugly Rendering Project (BURP)
Climateprediction.net
Collatz Conjecture
Correlizer
Cosmology@Home
DENIS@home
Docking@home
EDGeS@Home
EOn
Einstein@Home
Predictor@Home
Rosetta@home

ABC@home

  1. Martin, Greg and Winnie Miao. abc triples. (2014). DOI: 10.48550/ARXIV.1409.2974.

AQUA@home

  1. Karimi, Kamran, Neil Dickson and Firas Hamze. High-performance Physics Simulations Using Multi-core CPUs and GPGPUs in a Volunteer Computing Context. The International Journal of High Performance Computing Applications (2011). DOI: 10.1177/1094342010372928.
  2. Hamze, Firas, Neil Dickson and Kamran Karimi. Robust Parameter Selection for Parallel Tempering. (2010). DOI: 10.48550/ARXIV.1004.2840.
  3. Dickson, Neil G., Kamran Karimi and Firas Hamze. Importance of Explicit Vectorization for CPU and GPU Software Performance. (2010). DOI: 10.48550/ARXIV.1004.0024.
  4. Karimi, Kamran, Neil G. Dickson, Firas Hamze et al. Investigating the Performance of an Adiabatic Quantum Optimization Processor. (2010). DOI: 10.48550/ARXIV.1006.4147.

Asteroids@home

  1. Durech, J., J. Tonry, N. Erasmus, L. Denneau, A. N. Heinze, H. Flewelling and R. Vanco. Asteroid models reconstructed from ATLAS photometry. (2020). DOI: 10.48550/ARXIV.2010.01820.
  2. Durech, Josef, Josef Hanus and Radim Vanco. Inversion of asteroid photometry from Gaia DR2 and the Lowell Observatory photometric database. (2019). DOI: 10.48550/ARXIV.1909.09395.
  3. Durech, Josef, Josef Hanus and Victor Ali-Lagoa. Asteroid models reconstructed from the Lowell Photometric Database and WISE data. (2018). DOI: 10.48550/ARXIV.1807.02083.
  4. Hanuš, J., J. Ďurech, D. A. Oszkiewicz et al. New and updated convex shape models of asteroids based on optical data from a large collaboration network. Astronomy & Astrophysics (2016). DOI: 10.1051/0004-6361/201527441.
  5. Durech, J., J. Hanus, D. Oszkiewicz and R. Vanco. Asteroid models from the Lowell Photometric Database. (2016). DOI: 10.48550/ARXIV.1601.02909.
  6. Cibulková, H., J. Ďurech, D. Vokrouhlický, M. Kaasalainen and D. A. Oszkiewicz. Distribution of spin-axes longitudes and shape elongations of main-belt asteroids. Astronomy & Astrophysics (2016). DOI: 10.1051/0004-6361/201629192.
  7. Ďurech, J., J. Hanuš and R. Vančo. Asteroids@home—A BOINC distributed computing project for asteroid shape reconstruction. Astronomy and Computing (2015). DOI: 10.1016/j.ascom.2015.09.004.
  8. Durech, J., B. Carry, M. Delbo, M. Kaasalainen and M. Viikinkoski. Asteroid Models from Multiple Data Sources. (2015). DOI: 10.48550/ARXIV.1502.04816.
  9. Durech, Josef, J. Hanus, R. Vanco, D. Oszkiewicz and E. Bowell. New Asteroid Shape Models Derived from the Lowell Photometric Database. (2013).

Big and Ugly Rendering Project (BURP)

  1. Kantert, Jan, Christian Reinbold, Sven Tomforde and Christian Muller-Schloer. An Evaluation of Two Trust-Based Autonomic/Organic Grid Computing Systems for Volunteer-Based Distributed Rendering. 2016 IEEE International Conference on Autonomic Computing (ICAC) (2016). DOI: 10.1109/ICAC.2016.55.
  2. Kantert, Jan, Henning Spiegelberg, Sven Tomforde, Jorg Hahner and Christian Muller-Schloer. Distributed Rendering in an Open Self-Organised Trusted Desktop Grid. 2015 IEEE International Conference on Autonomic Computing (ICAC) (2015). DOI: 10.1109/ICAC.2015.66.

Climateprediction.net

  1. Allen, M., B. Booth, David Frame, J. Gregory, J. Kettleborough and Leonard Smith. Observational constraints on future climate: distinguishing robust from model-dependent statements of uncertainty in climate forecasting. (2022).
  2. Andrews, Timothy, Christopher J. Smith, Gunnar Myhre, Piers M. Forster, Robin Chadwick and Duncan Ackerley. Effective Radiative Forcing in a GCM With Fixed Surface Temperatures. Journal of Geophysical Research: Atmospheres (2021). DOI: 10.1029/2020JD033880.
  3. Aengenheyster, Matthias, Sarah Sparrow, Peter Watson, David Wallom, Laure Zanna and Myles Allen. Impact of sub-seasonal atmosphere-ocean interactions on extreme event statistics. (2021).
  4. Pham, Hoa X., Asaad Y. Shamseldin and Bruce W. Melville. Projection of future extreme precipitation: a robust assessment of downscaled daily precipitation. Natural Hazards (2021). DOI: 10.1007/s11069-021-04584-1.
  5. Di Capua, G., S. Sparrow, K. Kornhuber, E. Rousi, S. Osprey, D. Wallom, B. van den Hurk and D. Coumou. Drivers behind the summer 2010 wave train leading to Russian heatwave and Pakistan flooding. npj Climate and Atmospheric Science (2021). DOI: 10.1038/s41612-021-00211-9.
  6. Sparrow, Sarah, Andrew Bowery, Glenn D. Carver, Marcus O. Köhler, Pirkka Ollinaho, Florian Pappenberger, David Wallom and Antje Weisheimer. OpenIFS@home version 1: a citizen science project for ensemble weather and climate forecasting. Geoscientific Model Development (2021). DOI: 10.5194/gmd-14-3473-2021.
  7. Li, Sihan, Sarah N Sparrow, Friederike E L Otto et al. Anthropogenic climate change contribution to wildfire-prone weather conditions in the Cerrado and Arc of deforestation. Environmental Research Letters (2021). DOI: 10.1088/1748-9326/ac1e3a.
  8. Undorf, S., K. Allen, J. Hagg, S. Li, F. C. Lott, M. J. Metzger, S. N. Sparrow and S. F. B. Tett. Learning from the 2018 heatwave in the context of climate change: are high-temperature extremes important for adaptation in Scotland?. Environmental Research Letters (2020). DOI: 10.1088/1748-9326/ab6999.
  9. Li, Sihan, Friederike E L Otto, Luke J Harrington, Sarah N Sparrow and David C H Wallom. A pan-South-America assessment of avoided exposure to dangerous extreme precipitation by limiting to 1.5 °C warming. Environmental Research Letters (2020). DOI: 10.1088/1748-9326/ab50a2.
  10. Montes, Diego, Juan A. Añel, David C. H. Wallom, Peter Uhe, Pablo V. Caderno and Tomás F. Pena. Cloud Computing for Climate Modelling: Evaluation, Challenges and Benefits. Computers (2020). DOI: 10.3390/computers9020052.
  11. Watson, Peter, Sarah Sparrow, William Ingram et al. Multi-thousand member ensemble atmospheric simulations with global 60km resolution using climateprediction.net. (2020).
  12. Bussi, Gianbattista and Paul G. Whitehead. Impacts of droughts on low flows and water quality near power stations. Hydrological Sciences Journal (2020). DOI: 10.1080/02626667.2020.1724295.
  13. Rimi, Ruksana, Karsten Haustein, Emily Barbour, Sarah Sparrow, Sihan Li, David Wallom and Myles Allen. A Multi-model Assessment of the Changing Risks of Extreme Rainfall Events in Bangladesh under 1.5 and 2.0 degrees’ warmer worlds. (2020).
  14. Bevacqua, Emanuele, Ted Shepherd, Peter A. G. Watson, Sarah Sparrow, David C H Wallom and Daniel M Mitchell. Larger spatial footprint of wintertime total precipitation extremes in a warmer climate. (2020).
  15. Naveau, Philippe, Alexis Hannart and Aurélien Ribes. Statistical Methods for Extreme Event Attribution in Climate Science. Annual Review of Statistics and Its Application (2020). DOI: 10.1146/annurev-statistics-031219-041314.
  16. Di Capua, Giorgia, Kai Kornhuber, Eftychia Rousi, Sarah Sparrow, David Wallom and Dim Coumou. Wave-resonance fingerprint in the 2010 summer: a modelling experiment. (2020).
  17. Iyyanki, Murali Krishna V. and Prisilla Jayanthi. The Impact of Climate Change on Human Eyes. Urban Health Risk and Resilience in Asian Cities (2020).
  18. Leach, Nicholas J., Sihan Li, Sarah Sparrow, Geert Jan van Oldenborgh, Fraser C. Lott, Antje Weisheimer and Myles R. Allen. Anthropogenic Influence on the 2018 Summer Warm Spell in Europe: The Impact of Different Spatio-Temporal Scales. Bulletin of the American Meteorological Society (2020). DOI: 10.1175/BAMS-D-19-0201.1.
  19. Min, Seung-Ki, Yeon-Hee Kim, Sang-Min Lee, Sarah Sparrow, Sihan Li, Fraser C. Lott and Peter A. Stott. Quantifying Human Impact on the 2018 Summer Longest Heat Wave in South Korea. Bulletin of the American Meteorological Society (2020). DOI: 10.1175/BAMS-D-19-0151.1.
  20. Lo, Y. T. Eunice, Daniel M. Mitchell, Antonio Gasparrini et al. Increasing mitigation ambition to meet the Paris Agreement’s temperature goal avoids substantial heat-related mortality in U.S. cities. Science Advances (2019). DOI: 10.1126/sciadv.aau4373.
  21. Philip, Sjoukje, Sarah Sparrow, Sarah F. Kew et al. Attributing the 2017 Bangladesh floods from meteorological and hydrological perspectives. Hydrology and Earth System Sciences (2019). DOI: 10.5194/hess-23-1409-2019.
  22. Rimi, Ruksana H., Karsten Haustein, Emily J. Barbour, Richard G. Jones, Sarah N. Sparrow and Myles R. Allen. Evaluation of a large ensemble regional climate modelling system for extreme weather events analysis over Bangladesh. International Journal of Climatology (2019). DOI: 10.1002/joc.5931.
  23. Wehner, Michael F., Colin Zarzycki and Christina Patricola. Estimating the Human Influence on Tropical Cyclone Intensity as the Climate Changes. Hurricane Risk (2019).
  24. Hawkins, Linnia R., David E. Rupp, Doug J. McNeall, Sihan Li, Richard A. Betts, Philip W. Mote, Sarah N. Sparrow and David C. H. Wallom. Parametric Sensitivity of Vegetation Dynamics in the TRIFFID Model and the Associated Uncertainty in Projected Climate Change Impacts on Western U.S. Forests. Journal of Advances in Modeling Earth Systems (2019). DOI: 10.1029/2018MS001577.
  25. Baker, Hugh S., Tim Woollings, Chris E. Forest and Myles R. Allen. The Linear Sensitivity of the North Atlantic Oscillation and Eddy-Driven Jet to SSTs. Journal of Climate (2019). DOI: 10.1175/JCLI-D-19-0038.1.
  26. Baker, Hugh S., Tim Woollings, Cheikh Mbengue, Myles R. Allen, Christopher H. O’Reilly, Hideo Shiogama and Sarah Sparrow. Forced summer stationary waves: the opposing effects of direct radiative forcing and sea surface warming. Climate Dynamics (2019). DOI: 10.1007/s00382-019-04786-1.
  27. Marthews, T. R., R. G. Jones, S. J. Dadson, F. E. L. Otto, D. Mitchell, B. P. Guillod and M. R. Allen. The Impact of Human‐Induced Climate Change on Regional Drought in the Horn of Africa. Journal of Geophysical Research: Atmospheres (2019). DOI: 10.1029/2018JD030085.
  28. Gaupp, Franziska, Jim Hall, Dann Mitchell and Simon Dadson. Increasing risks of multiple breadbasket failure under 1.5 and 2 °C global warming. Agricultural Systems (2019). DOI: 10.1016/j.agsy.2019.05.010.
  29. Lawal, Kamoru A. and Dáithí A. Stone. On the Co-Variability between Climate Indices and the Potential Spread of Seasonal Climate Simulations over South African Provinces. Atmospheric and Climate Sciences (2019). DOI: 10.4236/acs.2019.93027.
  30. Min, Seung-Ki, Yeon-Hee Kim, In-Hong Park, Donghyun Lee, Sarah Sparrow, David Wallom and Dáithí Stone. Anthropogenic Contribution to the 2017 Earliest Summer Onset in South Korea. Bulletin of the American Meteorological Society (2019). DOI: 10.1175/BAMS-D-18-0096.1.
  31. Li, Sihan, David E. Rupp, Linnia Hawkins et al. Reducing climate model biases by exploring parameter space with large ensembles of climate model simulations and statistical emulation. Geoscientific Model Development (2019). DOI: 10.5194/gmd-12-3017-2019.
  32. Freychet, N., S. Sparrow, S. F. B. Tett, M. J. Mineter, G. C. Hegerl and D. C. H. Wallom. Impacts of Anthropogenic Forcings and El Niño on Chinese Extreme Temperatures. Advances in Atmospheric Sciences (2018). DOI: 10.1007/s00376-018-7258-8.
  33. Sparrow, Sarah, Qin Su, Fangxing Tian et al. Attributing human influence on the July 2017 Chinese heatwave: the influence of sea-surface temperatures. Environmental Research Letters (2018). DOI: 10.1088/1748-9326/aae356.
  34. Coxon, Gemma, Benoit Guillod, Jim Freer, Simon Dadson, Richard Jones, Thorsten Wagener, Ross Woods and Nicholas Howden. Projecting future changes in hydrological droughts in the UK : the impacts of bias correction and uncertainty in model predictions. (2018).
  35. Schaller, Nathalie, Sarah N. Sparrow, Neil R. Massey, Andy Bowery, Jonathan Miller, Simon Wilson, David C. H. Wallom and Friederike E. L. Otto. Ensemble of European regional climate simulations for the winter of 2013 and 2014 from HadAM3P-RM3P. Scientific Data (2018). DOI: 10.1038/sdata.2018.57.
  36. Guillod, Benoit P., Richard G. Jones, Simon J. Dadson et al. A large set of potential past, present and future hydro-meteorological time series for the UK. Hydrology and Earth System Sciences (2018). DOI: 10.5194/hess-22-611-2018.
  37. Harrington, Luke J. and Friederike E. L. Otto. Changing population dynamics and uneven temperature emergence combine to exacerbate regional exposure to heat extremes under 1.5 °C and 2 °C of warming. Environmental Research Letters (2018). DOI: 10.1088/1748-9326/aaaa99.
  38. Hirsch, Annette L., Benoit P. Guillod, Sonia I. Seneviratne et al. Biogeophysical Impacts of Land-Use Change on Climate Extremes in Low-Emission Scenarios: Results From HAPPI-Land. Earth's Future (2018). DOI: 10.1002/2017EF000744.
  39. Uhe, Peter, Sjoukje Philip, Sarah Kew et al. Attributing drivers of the 2016 Kenyan drought: 2016 KENYAN DROUGHT. International Journal of Climatology (2018). DOI: 10.1002/joc.5389.
  40. Rupp, David E. and Sihan Li. Less warming projected during heavy winter precipitation in the Cascades and Sierra Nevada: LESS WARMING DURING HEAVY PRECIPITATION. International Journal of Climatology (2017). DOI: 10.1002/joc.4963.
  41. Mitchell, Daniel, Paolo Davini, Ben Harvey et al. Assessing mid-latitude dynamics in extreme event attribution systems. Climate Dynamics (2017). DOI: 10.1007/s00382-016-3308-z.
  42. Guillod, Benoit P., Richard G. Jones, Alison L. Kay, Neil R. Massey, Sarah Sparrow, David C. H. Wallom and Simon S. Wilson. Managing the Risks, Impacts and Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential past and future climate time series for the UK from the weather@home2 model. (2017).
  43. Mulholland, David P., Keith Haines, Sarah N. Sparrow and David Wallom. Climate model forecast biases assessed with a perturbed physics ensemble. Climate Dynamics (2017). DOI: 10.1007/s00382-016-3407-x.
  44. Guillod, Benoit P., Richard G. Jones, Andy Bowery et al. weather@home 2: validation of an improved global–regional climate modelling system. Geoscientific Model Development (2017). DOI: 10.5194/gmd-10-1849-2017.
  45. Parker, Hannah R, Fraser C Lott, Rosalind J Cornforth, Daniel M Mitchell, Sarah Sparrow and David Wallom. A comparison of model ensembles for attributing 2012 West African rainfall. Environmental Research Letters (2017). DOI: 10.1088/1748-9326/aa5386.
  46. Parker, Hannah R., Emily Boyd, Rosalind J. Cornforth, Rachel James, Friederike E. L. Otto and Myles R. Allen. Stakeholder perceptions of event attribution in the loss and damage debate. Climate Policy (2017). DOI: 10.1080/14693062.2015.1124750.
  47. Rupp, David E., Sihan Li, Philip W. Mote, Karen M. Shell, Neil Massey, Sarah N. Sparrow, David C. H. Wallom and Myles R. Allen. Seasonal spatial patterns of projected anthropogenic warming in complex terrain: a modeling study of the western US. Climate Dynamics (2017). DOI: 10.1007/s00382-016-3200-x.
  48. Rupp, David E., Sihan Li, Philip W. Mote, Neil Massey, Sarah N. Sparrow and David C. H. Wallom. Influence of the Ocean and Greenhouse Gases on Severe Drought Likelihood in the Central United States in 2012. Journal of Climate (2017). DOI: 10.1175/JCLI-D-16-0294.1.
  49. Haustein, K, F E L Otto, P Uhe et al. Real-time extreme weather event attribution with forecast seasonal SSTs. Environmental Research Letters (2016). DOI: 10.1088/1748-9326/11/6/064006.
  50. van Oldenborgh, Geert Jan, Friederike E. L. Otto, Karsten Haustein and Krishna AchutaRao. The Heavy Precipitation Event of December 2015 in Chennai, India. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-16-0129.1.
  51. Uhe, P., F. E. L. Otto, K. Haustein, G. J. van Oldenborgh, A. D. King, D. C. H. Wallom, M. R. Allen and H. Cullen. Comparison of methods: Attributing the 2014 record European temperatures to human influences: COMPARING ATTRIBUTION, EUROPE 2014 TEMPERATURE. Geophysical Research Letters (2016). DOI: 10.1002/2016GL069568.
  52. Stott, Peter A., Nikolaos Christidis, Friederike E. L. Otto et al. Attribution of extreme weather and climate‐related events. WIREs Climate Change (2016). DOI: 10.1002/wcc.380.
  53. Sippel, S., F. E. L. Otto, M. Forkel et al. A novel bias correction methodology for climate impact simulations. Earth System Dynamics (2016). DOI: 10.5194/esd-7-71-2016.
  54. Añel, Juan, Tomas Pena, David Wallom and Diego Perez Montes. Enabling BOINC in Cloud Services: CPDN as Example. (2016).
  55. Otto, Friederike E. L. The art of attribution. Nature Climate Change (2016). DOI: 10.1038/nclimate2971.
  56. Guillod, Benoit P., Neil Massey, Friederike E. L. Otto, Myles R. Allen, Richard Jones and Jim W. Hall. Synthetic drought event sets: thousands of meteorological drought events for risk-based management under present and future conditions. (2016).
  57. Mote, Philip W., David E. Rupp, Sihan Li et al. Perspectives on the causes of exceptionally low 2015 snowpack in the western United States. Geophysical Research Letters (2016). DOI: 10.1002/2016GL069965.
  58. Karoly, David J., Mitchell T. Black, Andrew D. King and Michael R. Grose. The Roles of Climate Change and El Niño in the Record Low Rainfall in October 2015 in Tasmania, Australia. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-16-0139.1.
  59. Black, Mitchell T. and David J. Karoly. Southern Australia’s Warmest October on Record: The Role of ENSO and Climate Change. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-16-0124.1.
  60. Vautard, R, P Yiou, F Otto, P Stott, N Christidis, G J van Oldenborgh and N Schaller. Attribution of human-induced dynamical and thermodynamical contributions in extreme weather events. Environmental Research Letters (2016). DOI: 10.1088/1748-9326/11/11/114009.
  61. Schaller, Nathalie, Alison L. Kay, Rob Lamb et al. Human influence on climate in the 2014 southern England winter floods and their impacts. Nature Climate Change (2016). DOI: 10.1038/nclimate2927.
  62. Mote, Philip W., Myles R. Allen, Richard G. Jones, Sihan Li, Roberto Mera, David E. Rupp, Ahmed Salahuddin and Dean Vickers. Superensemble Regional Climate Modeling for the Western United States. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-14-00090.1.
  63. Hannart, A., J. Pearl, F. E. L. Otto, P. Naveau and M. Ghil. Causal Counterfactual Theory for the Attribution of Weather and Climate-Related Events. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-14-00034.1.
  64. Black, Mitchell T., David J. Karoly, Suzanne M. Rosier et al. The weather@home regional climate modelling project for Australia and New Zealand. Geoscientific Model Development (2016). DOI: 10.5194/gmd-9-3161-2016.
  65. Sippel, Sebastian, Dann Mitchell, Mitchell T. Black, Andrea J. Dittus, Luke Harrington, Nathalie Schaller and Friederike E.L. Otto. Combining large model ensembles with extreme value statistics to improve attribution statements of rare events. Weather and Climate Extremes (2015). DOI: 10.1016/j.wace.2015.06.004.
  66. Wesselink, Anna, Andrew Juan Challinor, James Watson et al. Equipped to deal with uncertainty in climate and impacts predictions: lessons from internal peer review. Climatic Change (2015). DOI: 10.1007/s10584-014-1213-1.
  67. Mera, Roberto, Neil Massey, David E. Rupp, Philip Mote, Myles Allen and Peter C. Frumhoff. Climate change, climate justice and the application of probabilistic event attribution to summer heat extremes in the California Central Valley. Climatic Change (2015). DOI: 10.1007/s10584-015-1474-3.
  68. Sippel, Sebastian, Jakob Zscheischler, Martin Heimann, Friederike E. L. Otto, Jonas Peters and Miguel D. Mahecha. Quantifying changes in climate variability and extremes: Pitfalls and their overcoming. Geophysical Research Letters (2015). DOI: 10.1002/2015GL066307.
  69. Rupp, David E., Sihan Li, Neil Massey, Sarah N. Sparrow, Philip W. Mote and Myles Allen. Anthropogenic influence on the changing likelihood of an exceptionally warm summer in Texas, 2011: Changing likelihood of warm summers.. Geophysical Research Letters (2015). DOI: 10.1002/2014GL062683.
  70. Otto, Friederike E. L., Emily Boyd, Richard G. Jones, Rosalind J. Cornforth, Rachel James, Hannah R. Parker and Myles R. Allen. Attribution of extreme weather events in Africa: a preliminary exploration of the science and policy implications. Climatic Change (2015). DOI: 10.1007/s10584-015-1432-0.
  71. Rosier, Suzanne, Sam Dean, Stephen Stuart, Trevor Carey-Smith, Mitchell T. Black and Neil Massey. Extreme Rainfall in Early July 2014 in Northland, New Zealand—Was There an Anthropogenic Influence?. Bulletin of the American Meteorological Society (2015). DOI: 10.1175/BAMS-D-15-00105.1.
  72. Otto, Friederike E. L., Suzanne M. Rosier, Myles R. Allen, Neil R. Massey, Cameron J. Rye and Jara Imbers Quintana. Attribution analysis of high precipitation events in summer in England and Wales over the last decade. Climatic Change (2015). DOI: 10.1007/s10584-014-1095-2.
  73. Li, Sihan, Philip W. Mote, David E. Rupp, Dean Vickers, Roberto Mera and Myles Allen. Evaluation of a Regional Climate Modeling Effort for the Western United States Using a Superensemble from Weather@home. Journal of Climate (2015). DOI: 10.1175/JCLI-D-14-00808.1.
  74. Lawal, Kamoru A., Dáithí A. Stone, Tolu Aina, Cameron Rye and Babatunde J. Abiodun. Trends in the potential spread of seasonal climate simulations over South Africa. International Journal of Climatology (2015). DOI: 10.1002/joc.4234.
  75. Otto, Friederike E. L., Karsten Haustein, Peter Uhe et al. Factors Other Than Climate Change, Main Drivers of 2014/15 Water Shortage in Southeast Brazil. Bulletin of the American Meteorological Society (2015). DOI: 10.1175/BAMS-D-15-00120.1.
  76. Hannart, A., C. Vera, B. Cerne and F. E. L. Otto. Causal Influence of Anthropogenic Forcings on the Argentinian Heat Wave of December 2013. Bulletin of the American Meteorological Society (2015). DOI: 10.1175/BAMS-D-15-00137.1.
  77. Volunteer Crowd Computing and Federated Cloud developments. (2015).
  78. Massey, N., R. Jones, F. E. L. Otto et al. weather@home—development and validation of a very large ensemble modelling system for probabilistic event attribution. Quarterly Journal of the Royal Meteorological Society (2015). DOI: 10.1002/qj.2455.
  79. Sippel, Sebastian, Peter Walton and Friederike E. L. Otto. Stakeholder Perspectives on the Attribution of Extreme Weather Events: An Explorative Enquiry. Weather, Climate, and Society (2015). DOI: 10.1175/WCAS-D-14-00045.1.
  80. Otto, Friederike E. L., David J. Frame, Alexander Otto and Myles R. Allen. Embracing uncertainty in climate change policy. Nature Climate Change (2015). DOI: 10.1038/nclimate2716.
  81. Otto, Friederike E. L. Attribution of extreme weather. Nature Geoscience (2015). DOI: 10.1038/ngeo2484.
  82. Thompson, Allen and Friederike E. L. Otto. Ethical and normative implications of weather event attribution for policy discussions concerning loss and damage. Climatic Change (2015). DOI: 10.1007/s10584-015-1433-z.
  83. Huntingford, Chris, Terry Marsh, Adam A. Scaife et al. Potential influences on the United Kingdom's floods of winter 2013/14. Nature Climate Change (2014). DOI: 10.1038/nclimate2314.
  84. Sippel, Sebastian and F E. L. Otto. Beyond climatological extremes - assessing how the odds of hydrometeorological extreme events in South-East Europe change in a warming climate. Climatic Change (2014). DOI: 10.1007/s10584-014-1153-9.
  85. Otto, Friederike E. L., Richard G. Jones, Kate Halladay and Myles R. Allen. Attribution of changes in precipitation patterns in African rainforests. Philosophical Transactions of the Royal Society B: Biological Sciences (2013). DOI: 10.1098/rstb.2012.0299.
  86. Peterson, Thomas C., Martin P. Hoerling, Peter A. Stott and Stephanie C. Herring. Explaining Extreme Events of 2012 from a Climate Perspective. Bulletin of the American Meteorological Society (2013). DOI: 10.1175/BAMS-D-13-00085.1.
  87. Otto, F. E. L., N. Massey, G. J. van Oldenborgh, R. G. Jones and M. R. Allen. Reconciling two approaches to attribution of the 2010 Russian heat wave: RUSSIAN HEAT WAVE 2010. Geophysical Research Letters (2012). DOI: 10.1029/2011GL050422.
  88. Rowlands, Daniel J., David J. Frame, Duncan Ackerley et al. Broad range of 2050 warming from an observationally constrained large climate model ensemble. Nature Geoscience (2012). DOI: 10.1038/ngeo1430.
  89. Ricke, Katharine L., Daniel J. Rowlands, William J. Ingram, David W. Keith and M. Granger Morgan. Effectiveness of stratospheric solar-radiation management as a function of climate sensitivity. Nature Climate Change (2012). DOI: 10.1038/nclimate1328.
  90. Peterson, Thomas C., Peter A. Stott and Stephanie Herring. Explaining Extreme Events of 2011 from a Climate Perspective. Bulletin of the American Meteorological Society (2012). DOI: 10.1175/BAMS-D-12-00021.1.
  91. Pall, Pardeep, Tolu Aina, Dáithí A. Stone, Peter A. Stott, Toru Nozawa, Arno G. J. Hilberts, Dag Lohmann and Myles R. Allen. Anthropogenic greenhouse gas contribution to flood risk in England and Wales in autumn 2000. Nature (2011). DOI: 10.1038/nature09762.
  92. Kay, A.L., S.M. Crooks, P. Pall and D.A. Stone. Attribution of Autumn/Winter 2000 flood risk in England to anthropogenic climate change: A catchment-based study. Journal of Hydrology (2011). DOI: 10.1016/j.jhydrol.2011.06.006.
  93. Fowler, Hayley J., Daniel Cooley, Stephan R. Sain and Milo Thurston. Detecting change in UK extreme precipitation using results from the climateprediction.net BBC climate change experiment. Extremes (2010). DOI: 10.1007/s10687-010-0101-y.
  94. Sanderson, Benjamin M., Karen M. Shell and William Ingram. Climate feedbacks determined using radiative kernels in a multi-thousand member ensemble of AOGCMs. Climate Dynamics (2010). DOI: 10.1007/s00382-009-0661-1.
  95. Ricke, Katharine L., M. Granger Morgan and Myles R. Allen. Regional climate response to solar-radiation management. Nature Geoscience (2010). DOI: 10.1038/ngeo915.
  96. Stone, Dáithí A., Myles R. Allen, Peter A. Stott, Pardeep Pall, Seung-Ki Min, Toru Nozawa and Seiji Yukimoto. The Detection and Attribution of Human Influence on Climate. Annual Review of Environment and Resources (2009). DOI: 10.1146/annurev.environ.040308.101032.
  97. Ackerley, Duncan, Eleanor J. Highwood and David J. Frame. Quantifying the effects of perturbing the physics of an interactive sulfur scheme using an ensemble of GCMs on the climateprediction.net platform: SULFUR CYCLE UNCERTAINTY QUANTIFICATION. Journal of Geophysical Research: Atmospheres (2009). DOI: 10.1029/2008JD010532.
  98. Frame, D.J, T Aina, C.M Christensen et al. The climate prediction .net BBC climate change experiment: design of the coupled model ensemble. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2009). DOI: 10.1098/rsta.2008.0240.
  99. Allen, Myles R., David J. Frame and Charles F. Mason. The case for mandatory sequestration. Nature Geoscience (2009). DOI: 10.1038/ngeo709.
  100. Lopez, Ana, Fai Fung, Mark New, Glenn Watts, Alan Weston and Robert L. Wilby. From climate model ensembles to climate change impacts and adaptation: A case study of water resource management in the southwest of England. Water Resources Research (2009). DOI: 10.1029/2008WR007499.
  101. Knutti, Reto, Stefan Krähenmann, David J. Frame and Myles R. Allen. Comment on “Heat capacity, time constant, and sensitivity of Earth's climate system” by S. E. Schwartz. Journal of Geophysical Research (2008). DOI: 10.1029/2007JD009473.
  102. Sanderson, Benjamin M., R. Knutti, T. Aina et al. Constraints on Model Response to Greenhouse Gas Forcing and the Role of Subgrid-Scale Processes. Journal of Climate (2008). DOI: 10.1175/2008JCLI1869.1.
  103. Sanderson, Benjamin M., C. Piani, W. J. Ingram, D. A. Stone and M. R. Allen. Towards constraining climate sensitivity by linear analysis of feedback patterns in thousands of perturbed-physics GCM simulations. Climate Dynamics (2008). DOI: 10.1007/s00382-007-0280-7.
  104. New, Mark, Ana Lopez, Suraje Dessai and Rob Wilby. Challenges in using probabilistic climate change information for impact assessments: an example from the water sector. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2007). DOI: 10.1098/rsta.2007.2080.
  105. Frame, D.J, N.E Faull, M.M Joshi and M.R Allen. Probabilistic climate forecasts and inductive problems. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2007). DOI: 10.1098/rsta.2007.2069.
  106. Knight, Christopher G., Sylvia H. E. Knight, Neil Massey et al. Association of parameter, software, and hardware variation with large-scale behavior across 57,000 climate models. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0608144104.
  107. Piani, C., B. Sanderson, F. Giorgi, D. J. Frame, C. Christensen and M. R. Allen. Regional probabilistic climate forecasts from a multithousand, multimodel ensemble of simulations. Journal of Geophysical Research: Atmospheres (2007). DOI: 10.1029/2007JD008712.
  108. Pall, P., M. R. Allen and D. A. Stone. Testing the Clausius–Clapeyron constraint on changes in extreme precipitation under CO2 warming. Climate Dynamics (2007). DOI: 10.1007/s00382-006-0180-2.
  109. Schwartz, Stephen E. Heat capacity, time constant, and sensitivity of Earth's climate system. Journal of Geophysical Research (2007). DOI: 10.1029/2007JD008746.
  110. Collins, Mat. Ensembles and probabilities: a new era in the prediction of climate change. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2007). DOI: 10.1098/rsta.2007.2068.
  111. Allen, Myles R. and David J. Frame. Call Off the Quest. Science (2007). DOI: 10.1126/science.1149988.
  112. Knutti, Reto, Gerald A. Meehl, Myles R. Allen and David A. Stainforth. Constraining Climate Sensitivity from the Seasonal Cycle in Surface Temperature. Journal of Climate (2006). DOI: 10.1175/JCLI3865.1.
  113. Allen, Myles, David Frame, Jamie Kettleborough and David Stainforth. Model error in weather and climate forecasting. Predictability of Weather and Climate (2006).
  114. Hegerl, Gabriele C., Thomas J. Crowley, William T. Hyde and David J. Frame. Climate sensitivity constrained by temperature reconstructions over the past seven centuries. Nature (2006). DOI: 10.1038/nature04679.
  115. Schellnhuber, Hans Joachim, Wolfgang Cramer, Wolfgang P. Cramer, Nebojsa Nakicenovic, Gary Yohe and Tom Wigley. Avoiding Dangerous Climate Change. (2006).
  116. Piani, C., D. J. Frame, D. A. Stainforth and M. R. Allen. Constraints on climate change from a multi-thousand member ensemble of simulations. Geophysical Research Letters (2005). DOI: 10.1029/2005GL024452.
  117. Stainforth, D. A., T. Aina, C. Christensen et al. Uncertainty in predictions of the climate response to rising levels of greenhouse gases. Nature (2005). DOI: 10.1038/nature03301.
  118. Frame, D. J., B. B. B. Booth, J. A. Kettleborough, D. A. Stainforth, J. M. Gregory, M. Collins and M. R. Allen. Constraining climate forecasts: The role of prior assumptions. Geophysical Research Letters (2005). DOI: 10.1029/2004GL022241.
  119. Stott, Peter A., D. A. Stone and M. R. Allen. Human contribution to the European heatwave of 2003. Nature (2004). DOI: 10.1038/nature03089.
  120. Joughin, Ian, Waleed Abdalati and Mark Fahnestock. Large fluctuations in speed on Greenland's Jakobshavn Isbræ glacier. Nature (2004). DOI: 10.1038/nature03130.
  121. Environmental Online Communication. Advanced Information and Knowledge Processing (2004).
  122. Murphy, James M., David M. H. Sexton, David N. Barnett, Gareth S. Jones, Mark J. Webb, Matthew Collins and David A. Stainforth. Quantification of modelling uncertainties in a large ensemble of climate change simulations. Nature (2004). DOI: 10.1038/nature02771.
  123. Allen, Myles R. and Richard Lord. The blame game. Nature (2004). DOI: 10.1038/432551a.
  124. Stainforth, David A., Myles R. Allen, David Frame, Jamie Kettleborough, Carl Christensen, Tolu Aina and Matthew Collins. Climateprediction.net: A Global Community for Research in Climate Physics. Environmental Online Communication (2004).
  125. Stainforth, D.A., D. Frame and J.P.R.B. Walton. Visualization For Public-Resource Climate Modeling. Eurographics / IEEE VGTC Symposium on Visualization (2004). DOI: 10.2312/VISSYM/VISSYM04/103-108.

Collatz Conjecture

  1. Barina, David. Convergence verification of the Collatz problem. The Journal of Supercomputing (2021). DOI: 10.1007/s11227-020-03368-x.

Correlizer

  1. Knoch, Tobias A. Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments–an evaluation and review framework of the 3D genome organization. Seminars in Cell & Developmental Biology (2019). DOI: 10.1016/j.semcdb.2018.07.012.
  2. Knoch, Tobias A. A Guided Protocol for Array Based T2C : A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture. Current Protocols in Human Genetics (2018). DOI: 10.1002/cphg.55.
  3. Rivero, Alejandro and Dario Ferrer. ISDEP, a fusion application deployed in the EDGeS project.. … workshop 30 March … (2010).
  4. Knoch, Tobias, Volkmar Baumgärtner, Luc de Zeeuw, Frank Grosveld and Kurt Egger. Large-scale resource sharing at public funded organizations. e-Human "Grid" Ecology.. (2009).
  5. Knoch, Tobias A., Markus Göker, Rudolf Lohner, Anis Abuseiris and Frank G. Grosveld. Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification. European Biophysics Journal (2009). DOI: 10.1007/s00249-009-0489-y.

Cosmology@Home

  1. Leclercq, F., B. Faure, G. Lavaux, B. D. Wandelt, A. H. Jaffe, A. F. Heavens and W. J. Percival. Perfectly parallel cosmological simulations using spatial comoving Lagrangian acceleration. Astronomy & Astrophysics (2020). DOI: 10.1051/0004-6361/202037995.
  2. Aghanim, N., Y. Akrami, M. Ashdown et al. Planck intermediate results - LI. Features in the cosmic microwave background temperature power spectrum and shifts in cosmological parameters. Astronomy & Astrophysics (2017). DOI: 10.1051/0004-6361/201629504.
  3. DockerCon EU 2015: Finding a Theory of the Universe with Docker and V…. (2015).
  4. Fendt, William A. and Benjamin D. Wandelt. Pico: Parameters for the Impatient Cosmologist. The Astrophysical Journal (2007). DOI: 10.1086/508342.
  5. Fendt, William A. and Benjamin D. Wandelt. Computing High Accuracy Power Spectra with Pico. (2007). DOI: 10.48550/ARXIV.0712.0194.

DENIS@home

  1. Monasterio, Violeta, Joel Castro-Mur and Jesús Carro. DENIS: Solving cardiac electrophysiological simulations with volunteer computing. PLOS ONE (2018). DOI: 10.1371/journal.pone.0205568.
  2. Carro, Jesús, José F Rodríguez-Matas and Esther Pueyo. A Methodology to Improve Human Ventricular Models for the Investigation of Cardiac Arrhythmias. Biophysical Journal (2017). DOI: 10.1016/j.bpj.2016.11.2183.
  3. Castro, Joel, Violeta Monasterio and Jesus Carro. Volunteer Computing Approach for the Collaborative Simulation of Electrophysiological Models. 2016 IEEE 25th International Conference on Enabling Technologies: Infrastructure for Collaborative Enterprises (WETICE) (2016). DOI: 10.1109/WETICE.2016.34.

Docking@home

  1. Zhang, Boyu, Trilce Estrada, Pietro Cicotti, Pavan Balaji and Michela Taufer. Enabling scalable and accurate clustering of distributed ligand geometries on supercomputers. Parallel Computing (2017). DOI: 10.1016/j.parco.2017.02.005.
  2. Zhang, Boyu, Trilce Estrada, Pietro Cicotti and Michela Taufer. On Efficiently Capturing Scientific Properties in Distributed Big Data without Moving the Data: A Case Study in Distributed Structural Biology Using MapReduce. 2013 IEEE 16th International Conference on Computational Science and Engineering (CSE) (2013). DOI: 10.1109/CSE.2013.28.
  3. Estrada, Trilce, Kathleen L. Pusecker, Manuel R. Torres, Joanne Cohoon and Michela Taufer. Benchmarking Gender Differences in Volunteer Computing Projects. 2013 IEEE 9th International Conference on eScience (eScience) (2013). DOI: 10.1109/eScience.2013.29.
  4. ExSciTecH: Expanding Volunteer Computing to Explore Science, Technology, and Health. (2012).
  5. Estrada, T., B. Zhang, P. Cicotti, R.S. Armen and M. Taufer. A scalable and accurate method for classifying protein–ligand binding geometries using a MapReduce approach. Computers in Biology and Medicine (2012). DOI: 10.1016/j.compbiomed.2012.05.001.
  6. Estrada, Trilce, Boyu Zhang, Michela Taufer, Pietro Cicotti and Roger Armen. Reengineering High-throughput Molecular Datasets for Scalable Clustering Using MapReduce. 2012 IEEE 14th Int'l Conf. on High Performance Computing and Communication (HPCC) & 2012 IEEE 9th Int'l Conf. on Embedded Software and Systems (ICESS) (2012). DOI: 10.1109/HPCC.2012.54.
  7. Rahaman, Obaidur, Trilce P. Estrada, Douglas J. Doren, Michela Taufer, Charles L. Brooks and Roger S. Armen. Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy. Journal of Chemical Information and Modeling (2011). DOI: 10.1021/ci1003009.
  8. Estrada, Trilce and Michela Taufer. Providing Quality of Science in Volunteer Computing. Communication (HPCC) (2011). DOI: 10.1109/HPCC.2011.19.
  9. Luo, Wenjia, Jianfeng Pei and Yushan Zhu. A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity. Journal of Molecular Modeling (2010). DOI: 10.1007/s00894-009-0598-7.
  10. Estrada, Trlce, Roger Armen and Michela Taufer. Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing. the First ACM International Conference (2010). DOI: 10.1145/1854776.1854807.
  11. Taufer, M., R. Armen, Jianhan Chen, P. Teller and C. Brooks. Computational multiscale modeling in protein--ligand docking. IEEE Engineering in Medicine and Biology Magazine (2009). DOI: 10.1109/MEMB.2009.931789.
  12. Atlas, James, Trilce Estrada, Keith Decker and Michela Taufer. Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing Using Constraint Optimization. Computational Science – ICCS 2009 (2009).
  13. Estrada, Trilce, Michela Taufer and David P. Anderson. Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC. Journal of Grid Computing (2009). DOI: 10.1007/s10723-009-9126-3.
  14. Estrada, Trilce, Michela Taufer, Kevin Reed and David P. Anderson. EmBOINC: An emulator for performance analysis of BOINC projects. Distributed Processing (IPDPS) (2009). DOI: 10.1109/IPDPS.2009.5161135.
  15. Estrada, Trilce, Michela Taufer and Kevin Reed. Modeling Job Lifespan Delays in Volunteer Computing Projects. 2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid (2009). DOI: 10.1109/CCGRID.2009.69.
  16. Estrada, Trilce, Olac Fuentes and Michela Taufer. A distributed evolutionary method to design scheduling policies for volunteer computing. the 2008 conference (2008). DOI: 10.1145/1366230.1366282.
  17. Lopez, Guillermo A., Michela Taufer and Patricia J. Teller. Evaluation of IEEE 754 floating-point arithmetic compliance across a wide range of heterogeneous computers. the 2007 conference (2007). DOI: 10.1145/1347787.1347793.
  18. Taufer, M., A. Kerstens, T. P. Estrada, D. A. Flores, R. Zamudio, P. J. Teller, R. Armen and C. L. Brooks. Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. 2007 IEEE International Parallel and Distributed Processing Symposium (2007). DOI: 10.1109/IPDPS.2007.370668.
  19. Taufer, Michela, Andre Kerstens, Trilce Estrada, David Flores and Patricia J. Teller. SimBA: A Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. 21st International Workshop on Principles of Advanced and Distributed Simulation (2007). DOI: 10.1109/PADS.2007.27.
  20. Estrada, Trilce, David A. Flores, Michela Taufer, Patricia J. Teller, Andre Kerstens and David P. Anderson. The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects. 2006 Second IEEE International Conference on e-Science and Grid Computing (2006). DOI: 10.1109/E-SCIENCE.2006.261172.
  21. Taufer, M., M. Crowley, D. J. Price, A. A. Chien and C. L. Brooks. Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. Concurrency and Computation: Practice and Experience (2005). DOI: 10.1002/cpe.949.
  22. Taufer, M., D. Anderson, P. Cicotti and C.L. Brooks. Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. 19th IEEE International Parallel and Distributed Processing Symposium (2005). DOI: 10.1109/IPDPS.2005.247.
  23. Taufer, M., M. Crowley, D. Price, A.A. Chien and C.L. Brooks. Study of a highly accurate and fast protein-ligand docking algorithm based on molecular dynamics. 18th International Parallel and Distributed Processing Symposium, 2004. (2004). DOI: 10.1109/IPDPS.2004.1303203.

EDGeS@Home

  1. Kacsuk, P., Zoltan Farkas, József Kovács et al. Desktop grid in the era of cloud computing. (2015).
  2. Fedak, Gilles. Contributions to Desktop Grid Computing. (2015).
  3. Delamare, Simon, Gilles Fedak, Derrick Kondo and Oleg Lodygensky. SpeQuloS: a QoS service for hybrid and elastic computing infrastructures. Cluster Computing (2014). DOI: 10.1007/s10586-013-0283-6.
  4. Visegrádi, Ádám, József Kovács and Peter Kacsuk. Efficient extension of gLite VOs with BOINC based desktop grids. Future Generation Computer Systems (2014). DOI: 10.1016/j.future.2013.10.012.
  5. Marosi, Attila, József Kovács and Peter Kacsuk. Towards a volunteer cloud system. Future Generation Computer Systems (2013). DOI: 10.1016/j.future.2012.03.013.
  6. Delamare, Simon, Gilles Fedak, Derrick Kondo, Oleg Lodygensky, Péter Kacsuk, Jozsef Kovacs and Filipe Araujo. Advanced QoS Prototype for the EDGI Infrastructure. (2013).
  7. Delamare, Simon, Gilles Fedak, Derrick Kondo, O. Lodygensky, Péter Kacsuk, József Kovács and Filipe Araujo. Intermediate QoS Prototype for the EDGI Infrastructure. (2013).
  8. Terstyanszky, Gabor, Tamas Kiss, Tamas Kukla, Zsolt Lichtenberger, Stephen Winter, Pamela Greenwell, Sharron McEldowney and Hans Heindl. Application repository and science gateway for running molecular docking and dynamics simulations. Studies in Health Technology and Informatics (2012).
  9. Kacsuk, P., Z. Farkas and Z. Balaton. EDGeS Bridge Technologies to Interconnect Service and Desktop Grids. Remote Instrumentation Services on the e-Infrastructure (2011).
  10. Velasco, J. L., F. Castejón and A. Tarancón. Finite orbit width effect in ion collisional transport in TJ-II. Physics of Plasmas (2009). DOI: 10.1063/1.3126583.
  11. Fedak, Gilles, Haiwu He, Oleg Lodygensky et al. EDGeS: A Bridge between Desktop Grids and Service Grids. 2008 Third ChinaGrid Annual Conference (CHINAGRID) (2008). DOI: 10.1109/ChinaGrid.2008.44.
  12. Antolí, B., Francisco Castejón, A. Giner et al. ZIVIS: A City Computing Platform Based on Volunteer Computing. (2007).

EOn

  1. Chill, Samuel T, Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude Berthet, Andreas Pedersen, Hannes Jónsson and Graeme Henkelman. EON: software for long time simulations of atomic scale systems. Modelling and Simulation in Materials Science and Engineering (2014). DOI: 10.1088/0965-0393/22/5/055002.
  2. Pedersen, Andreas, Graeme Henkelman, Jakob Schiøtz and Hannes Jónsson. Long time scale simulation of a grain boundary in copper. New Journal of Physics (2009). DOI: 10.1088/1367-2630/11/7/073034.
  3. Mei, Donghai, Lijun Xu and Graeme Henkelman. Potential Energy Surface of Methanol Decomposition on Cu(110). The Journal of Physical Chemistry C (2009). DOI: 10.1021/jp808211q.
  4. Xu, Lijun, Donghai Mei and Graeme Henkelman. Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100). The Journal of Chemical Physics (2009). DOI: 10.1063/1.3281688.
  5. Xu, Lijun and Graeme Henkelman. Adaptive kinetic Monte Carlo for first-principles accelerated dynamics. The Journal of Chemical Physics (2008). DOI: 10.1063/1.2976010.
  6. Henkelman, Graeme and Hannes Jónsson. Multiple Time Scale Simulations of Metal Crystal Growth Reveal the Importance of Multiatom Surface Processes. Physical Review Letters (2003). DOI: 10.1103/PhysRevLett.90.116101.

Einstein@Home

  1. Ming, J., M. A. Papa, H.-B. Eggenstein, B. Machenschalk, B. Steltner, R. Prix, B. Allen and O. Behnke. Results From an Einstein@Home Search for Continuous Gravitational Waves From G347.3 at Low Frequencies in LIGO O2 Data. The Astrophysical Journal (2022). DOI: 10.3847/1538-4357/ac35cb.
  2. Parent, E., H. Sewalls, P. C. C. Freire et al. Study of 72 Pulsars Discovered in the PALFA Survey: Timing Analysis, Glitch Activity, Emission Variability, and a Pulsar in an Eccentric Binary. The Astrophysical Journal (2022). DOI: 10.3847/1538-4357/ac375d.
  3. Steltner, B., M. A. Papa, H.-B. Eggenstein et al. Einstein@Home All-sky Search for Continuous Gravitational Waves in LIGO O2 Public Data. The Astrophysical Journal (2021). DOI: 10.3847/1538-4357/abc7c9.
  4. Nieder, L., B. Allen, C. J. Clark and H. J. Pletsch. Exploiting Orbital Constraints from Optical Data to Detect Binary Gamma-Ray Pulsars. The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/abaf53.
  5. Clark, C. J., L. Nieder, G. Voisin et al. Einstein@Home Discovery of the Gamma-ray Millisecond Pulsar PSR J2039-5617 Confirms Its Predicted Redback Nature. (2020). DOI: 10.48550/ARXIV.2007.14849.
  6. Nieder, L., C. J. Clark, D. Kandel et al. Discovery of a Gamma-Ray Black Widow Pulsar by GPU-accelerated Einstein@Home. The Astrophysical Journal Letters (2020). DOI: 10.3847/2041-8213/abbc02.
  7. Papa, M. A., J. Ming, E. V. Gotthelf et al. Search for Continuous Gravitational Waves from the Central Compact Objects in Supernova Remnants Cassiopeia A, Vela Jr., and G347.3–0.5. The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/ab92a6.
  8. Walsh, Sinéad, Karl Wette, Maria Alessandra Papa and Reinhard Prix. Optimizing the choice of analysis method for all-sky searches for continuous gravitational waves with Einstein@Home. Physical Review D (2019). DOI: 10.1103/PhysRevD.99.082004.
  9. Ming, J., M. A. Papa, A. Singh et al. Results from an Einstein@Home search for continuous gravitational waves from Cassiopeia A, Vela Jr., and G347.3. Physical Review D (2019). DOI: 10.1103/PhysRevD.100.024063.
  10. Wu, J., C. J. Clark, H. J. Pletsch et al. The Einstein@Home Gamma-ray Pulsar Survey. II. Source Selection, Spectral Analysis, and Multiwavelength Follow-up. The Astrophysical Journal (2018). DOI: 10.3847/1538-4357/aaa411.
  11. Clark, Colin J., Holger J. Pletsch, Jason Wu et al. Einstein@Home discovers a radio-quiet gamma-ray millisecond pulsar. Science Advances (2018). DOI: 10.1126/sciadv.aao7228.
  12. Ming, Jing, Maria Alessandra Papa, Badri Krishnan et al. Optimally setting up directed searches for continuous gravitational waves in Advanced LIGO O1 data. Physical Review D (2018). DOI: 10.1103/PhysRevD.97.024051.
  13. Abbott, B. P., R. Abbott, T. D. Abbott et al. First low-frequency Einstein@Home all-sky search for continuous gravitational waves in Advanced LIGO data. Physical Review D (2017). DOI: 10.1103/PhysRevD.96.122004.
  14. Zhu, Sylvia J., Maria Alessandra Papa and Sinéad Walsh. New veto for continuous gravitational wave searches. Physical Review D (2017). DOI: 10.1103/PhysRevD.96.124007.
  15. Singh, Avneet, Maria Alessandra Papa, Heinz-Bernd Eggenstein and Sinéad Walsh. Adaptive clustering procedure for continuous gravitational wave searches. Physical Review D (2017). DOI: 10.1103/PhysRevD.96.082003.
  16. Clark, C. J., J. Wu, H. J. Pletsch et al. THE EINSTEIN@HOME GAMMA-RAY PULSAR SURVEY. I. SEARCH METHODS, SENSITIVITY, AND DISCOVERY OF NEW YOUNG GAMMA-RAY PULSARS. The Astrophysical Journal (2017). DOI: 10.3847/1538-4357/834/2/106.
  17. Zhu, Sylvia J., Maria Alessandra Papa and Sinéad Walsh. A new veto for continuous gravitational wave searches. (2017). DOI: 10.48550/ARXIV.1707.05268.
  18. Lyne, A. G., B. W. Stappers, S. Bogdanov et al. TIMING OF 29 PULSARS DISCOVERED IN THE PALFA SURVEY. The Astrophysical Journal (2017). DOI: 10.3847/1538-4357/834/2/137.
  19. Zhu, Sylvia J., Maria Alessandra Papa, Heinz-Bernd Eggenstein et al. An Einstein@home search for continuous gravitational waves from Cassiopeia A. (2016). DOI: 10.48550/ARXIV.1608.07589.
  20. Lazarus, P., P. C. C. Freire, B. Allen et al. EINSTEIN@HOME DISCOVERY OF A DOUBLE NEUTRON STAR BINARY IN THE PALFA SURVEY. The Astrophysical Journal (2016). DOI: 10.3847/0004-637X/831/2/150.
  21. Abbott, B. P., R. Abbott, T. D. Abbott et al. Results of the deepest all-sky survey for continuous gravitational waves on LIGO S6 data running on the Einstein@Home volunteer distributed computing project. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.102002.
  22. Clark, C. J., H. J. Pletsch, J. Wu et al. THE BRAKING INDEX OF A RADIO-QUIET GAMMA-RAY PULSAR. The Astrophysical Journal (2016). DOI: 10.3847/2041-8205/832/1/L15.
  23. Singh, Avneet, Maria Alessandra Papa, Heinz-Bernd Eggenstein et al. Results of an all-sky high-frequency Einstein@Home search for continuous gravitational waves in LIGO’s fifth science run. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.064061.
  24. Papa, Maria Alessandra, Heinz-Bernd Eggenstein, Sinéad Walsh et al. Hierarchical follow-up of subthreshold candidates of an all-sky Einstein@Home search for continuous gravitational waves on LIGO sixth science run data. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.122006.
  25. Zhu, Sylvia J., Maria Alessandra Papa, Heinz-Bernd Eggenstein et al. Einstein@Home search for continuous gravitational waves from Cassiopeia A. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.082008.
  26. Clark, C. J., H. J. Pletsch, J. Wu et al. PSR J1906+0722: AN ELUSIVE GAMMA-RAY PULSAR. The Astrophysical Journal (2015). DOI: 10.1088/2041-8205/809/1/L2.
  27. Knispel, B., A. G. Lyne, B. W. Stappers et al. Einstein@Home DISCOVERY OF A PALFA MILLISECOND PULSAR IN AN ECCENTRIC BINARY ORBIT. The Astrophysical Journal (2015). DOI: 10.1088/0004-637X/806/1/140.
  28. Shaltev, M., P. Leaci, M. A. Papa and R. Prix. Fully coherent follow-up of continuous gravitational-wave candidates: An application to Einstein@Home results. Physical Review D (2014). DOI: 10.1103/PhysRevD.89.124030.
  29. Aasi, J., J. Abadie, B. P. Abbott et al. Einstein@Home all-sky search for periodic gravitational waves in LIGO S5 data. Physical Review D (2013). DOI: 10.1103/PhysRevD.87.042001.
  30. Allen, B., B. Knispel, J. M. Cordes et al. THE EINSTEIN@HOME SEARCH FOR RADIO PULSARS AND PSR J2007+2722 DISCOVERY. The Astrophysical Journal (2013). DOI: 10.1088/0004-637X/773/2/91.
  31. Knispel, B., R. P. Eatough, H. Kim et al. EINSTEIN@HOME DISCOVERY OF 24 PULSARS IN THE PARKES MULTI-BEAM PULSAR SURVEY. The Astrophysical Journal (2013). DOI: 10.1088/0004-637X/774/2/93.
  32. Pletsch, H. J., L. Guillemot, B. Allen et al. EINSTEIN@HOME DISCOVERY OF FOUR YOUNG GAMMA-RAY PULSARS IN FERMI LAT DATA. The Astrophysical Journal (2013). DOI: 10.1088/2041-8205/779/1/L11.
  33. Knispel, B., P. Lazarus, B. Allen et al. ARECIBO PALFA SURVEY AND EINSTEIN@HOME: BINARY PULSAR DISCOVERY BY VOLUNTEER COMPUTING. The Astrophysical Journal (2011). DOI: 10.1088/2041-8205/732/1/L1.
  34. Knispel, B., B. Allen, J. M. Cordes et al. Pulsar Discovery by Global Volunteer Computing. Science (2010). DOI: 10.1126/science.1195253.
  35. Abbott, B., R. Abbott, R. Adhikari et al. Einstein@Home search for periodic gravitational waves in LIGO S4 data. Physical Review D (2009). DOI: 10.1103/PhysRevD.79.022001.
  36. Pletsch, Holger J. and Bruce Allen. Exploiting Large-Scale Correlations to Detect Continuous Gravitational Waves. Physical Review Letters (2009). DOI: 10.1103/PhysRevLett.103.181102.
  37. Breitbart, Jens and Gaurav Khanna. An Exploration of CUDA and CBEA for a Gravitational Wave Data- Analysis Application (Einstein@Home). The Open Astronomy Journal (2009). DOI: 10.2174/1874381101004010154.
  38. Abbott, B. P., R. Abbott, R. Adhikari et al. Einstein@Home search for periodic gravitational waves in early S5 LIGO data. Physical Review D (2009). DOI: 10.1103/PhysRevD.80.042003.

Predictor@Home

  1. Taufer, M., Chahm An, A. Kerstens and C.L. Brooks III. Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing. IEEE Transactions on Parallel and Distributed Systems (2006). DOI: 10.1109/TPDS.2006.110.
  2. Taufer, M., D. Anderson, P. Cicotti and C.L. Brooks. Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. 19th IEEE International Parallel and Distributed Processing Symposium (2005). DOI: 10.1109/IPDPS.2005.247.
  3. Taufer, M., P.J. Teller, D.P. Anderson and C.L. Brooks. Metrics for effective resource management in global computing environments. First International Conference on e-Science and Grid Computing (e-Science'05) (2005). DOI: 10.1109/E-SCIENCE.2005.58.

Rosetta@home

  1. Courbet, A., J. Hansen, Y. Hsia et al. Computational design of mechanically coupled axle-rotor protein assemblies. Science (2022). DOI: 10.1126/science.abm1183.
  2. Hunt, Andrew C., James Brett Case, Young-Jun Park et al. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. (2021). DOI: 10.1101/2021.07.07.451375.
  3. Norn, Christoffer, Basile I. M. Wicky, David Juergens et al. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2017228118.
  4. Hsia, Yang, Rubul Mout, William Sheffler et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nature Communications (2021). DOI: 10.1038/s41467-021-22276-z.
  5. Quijano-Rubio, Alfredo, Hsien-Wei Yeh, Jooyoung Park et al. De novo design of modular and tunable protein biosensors. Nature (2021). DOI: 10.1038/s41586-021-03258-z.
  6. Brunette, Tj, Matthew J. Bick, Jesse M. Hansen, Cameron M. Chow, Justin M. Kollman and David Baker. Modular repeat protein sculpting using rigid helical junctions. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1908768117.
  7. Cao, Longxing, Inna Goreshnik, Brian Coventry et al. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science (2020). DOI: 10.1126/science.abd9909.
  8. Yang, Jianyi, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov and David Baker. Improved protein structure prediction using predicted interresidue orientations. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1914677117.
  9. Leman, Julia Koehler, Brian D. Weitzner, P. Douglas Renfrew et al. Better together: Elements of successful scientific software development in a distributed collaborative community. PLOS Computational Biology (2020). DOI: 10.1371/journal.pcbi.1007507.
  10. Wei, Kathy Y., Danai Moschidi, Matthew J. Bick et al. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1914808117.
  11. Mulligan, Vikram Khipple, Christine S. Kang, Michael R. Sawaya et al. Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Science (2020). DOI: 10.1002/pro.3974.
  12. Silva, Daniel-Adriano, Shawn Yu, Umut Ulge et al. De novo design of potent and selective mimics of IL-2 and IL-15. Nature (2019). DOI: 10.1038/s41586-018-0830-7.
  13. Pyles, Harley, Shuai Zhang, James J. De Yoreo and David Baker. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature (2019). DOI: 10.1038/s41586-019-1361-6.
  14. Lu, Peilong, Duyoung Min, Frank DiMaio et al. Accurate computational design of multipass transmembrane proteins. Science (2018). DOI: 10.1126/science.aaq1739.
  15. Park, Hahnbeom, David E. Kim, Sergey Ovchinnikov, David Baker and Frank DiMaio. Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins: Structure, Function, and Bioinformatics (2018). DOI: 10.1002/prot.25387.
  16. Dou, Jiayi, Anastassia A. Vorobieva, William Sheffler et al. De novo design of a fluorescence-activating β-barrel. Nature (2018). DOI: 10.1038/s41586-018-0509-0.
  17. Marcos, Enrique, Tamuka M. Chidyausiku, Andrew C. McShan et al. De novo design of a non-local β-sheet protein with high stability and accuracy. Nature Structural & Molecular Biology (2018). DOI: 10.1038/s41594-018-0141-6.
  18. Ovchinnikov, Sergey, Hahnbeom Park, David E. Kim, Frank DiMaio and David Baker. Protein structure prediction using Rosetta in CASP12. Proteins: Structure, Function, and Bioinformatics (2018). DOI: 10.1002/prot.25390.
  19. Shen, Hao, Jorge A. Fallas, Eric Lynch et al. De novo design of self-assembling helical protein filaments. Science (2018). DOI: 10.1126/science.aau3775.
  20. Ovchinnikov, Sergey, Hahnbeom Park, Neha Varghese et al. Protein structure determination using metagenome sequence data. Science (2017). DOI: 10.1126/science.aah4043.
  21. Rocklin, Gabriel J., Tamuka M. Chidyausiku, Inna Goreshnik et al. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science (2017). DOI: 10.1126/science.aan0693.
  22. Hosseinzadeh, Parisa, Gaurav Bhardwaj, Vikram Khipple Mulligan et al. Comprehensive computational design of ordered peptide macrocycles. Science (2017). DOI: 10.1126/science.aap7577.
  23. Huang, Po-Ssu, Kaspar Feldmeier, Fabio Parmeggiani, D. Alejandro Fernandez Velasco, Birte Höcker and David Baker. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology (2016). DOI: 10.1038/nchembio.1966.
  24. Bhardwaj, Gaurav, Vikram Khipple Mulligan, Christopher D. Bahl et al. Accurate de novo design of hyperstable constrained peptides. Nature (2016). DOI: 10.1038/nature19791.
  25. Bale, Jacob B., Shane Gonen, Yuxi Liu et al. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science (2016). DOI: 10.1126/science.aaf8818.
  26. Ovchinnikov, Sergey, David E. Kim, Ray Yu-Ruei Wang, Yuan Liu, Frank DiMaio and David Baker. Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. Proteins: Structure, Function, and Bioinformatics (2016). DOI: 10.1002/prot.24974.
  27. Hsia, Yang, Jacob B. Bale, Shane Gonen et al. Design of a hyperstable 60-subunit protein icosahedron. Nature (2016). DOI: 10.1038/nature18010.
  28. Boyken, Scott E., Zibo Chen, Benjamin Groves et al. De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity. Science (2016). DOI: 10.1126/science.aad8865.
  29. Ovchinnikov, Sergey, Lisa Kinch, Hahnbeom Park et al. Large-scale determination of previously unsolved protein structures using evolutionary information. eLife (2015). DOI: 10.7554/eLife.09248.
  30. Antala, Sagar, Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker and Robert E. Dempski. Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4 *. Journal of Biological Chemistry (2015). DOI: 10.1074/jbc.M114.617613.
  31. Siegel, Justin B., Amanda Lee Smith, Sean Poust et al. Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences (2015). DOI: 10.1073/pnas.1500545112.
  32. Park, Keunwan, Betty W. Shen, Fabio Parmeggiani, Po-Ssu Huang, Barry L. Stoddard and David Baker. Control of repeat-protein curvature by computational protein design. Nature Structural & Molecular Biology (2015). DOI: 10.1038/nsmb.2938.
  33. Parmeggiani, Fabio, Po-Ssu Huang, Sergey Vorobiev et al. A General Computational Approach for Repeat Protein Design. Journal of Molecular Biology (2015). DOI: 10.1016/j.jmb.2014.11.005.
  34. Brunette, T. J., Fabio Parmeggiani, Po-Ssu Huang et al. Exploring the repeat protein universe through computational protein design. Nature (2015). DOI: 10.1038/nature16162.
  35. Pearson, A. D., J. H. Mills, Y. Song, F. Nasertorabi, G. W. Han, D. Baker, R. C. Stevens and P. G. Schultz. Trapping a transition state in a computationally designed protein bottle. Science (2015). DOI: 10.1126/science.aaa2424.
  36. Ovchinnikov, Sergey, Hetunandan Kamisetty and David Baker. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information. eLife (2014). DOI: 10.7554/eLife.02030.
  37. Kim, David E., Frank DiMaio, Ray Yu-Ruei Wang, Yifan Song and David Baker. One contact for every twelve residues allows robust and accurate topology-level protein structure modeling: Contact Guided Protein Structure Prediction. Proteins: Structure, Function, and Bioinformatics (2014). DOI: 10.1002/prot.24374.
  38. King, Chris, Esteban N. Garza, Ronit Mazor, Jonathan L. Linehan, Ira Pastan, Marion Pepper and David Baker. Removing T-cell epitopes with computational protein design. Proceedings of the National Academy of Sciences (2014). DOI: 10.1073/pnas.1321126111.
  39. Conway, Patrick, Michael D. Tyka, Frank DiMaio, David E. Konerding and David Baker. Relaxation of backbone bond geometry improves protein energy landscape modeling: Relaxation of Backbone Bond Geometry. Protein Science (2014). DOI: 10.1002/pro.2389.
  40. King, Neil P., Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates and David Baker. Accurate design of co-assembling multi-component protein nanomaterials. Nature (2014). DOI: 10.1038/nature13404.
  41. Huang, Po-Ssu, Gustav Oberdorfer, Chunfu Xu et al. High thermodynamic stability of parametrically designed helical bundles. Science (2014). DOI: 10.1126/science.1257481.
  42. Griss, Rudolf, Alberto Schena, Luc Reymond, Luc Patiny, Dominique Werner, Christine E. Tinberg, David Baker and Kai Johnsson. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nature Chemical Biology (2014). DOI: 10.1038/nchembio.1554.
  43. Strauch, Eva-Maria, Sarel J. Fleishman and David Baker. Computational design of a pH-sensitive IgG binding protein. Proceedings of the National Academy of Sciences (2014). DOI: 10.1073/pnas.1313605111.
  44. Baker, David. Protein folding, structure prediction and design. Biochemical Society Transactions (2014). DOI: 10.1042/BST20130055.
  45. Procko, Erik, Geoffrey Y. Berguig, Betty W. Shen et al. A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells. Cell (2014). DOI: 10.1016/j.cell.2014.04.034.
  46. DiMaio, Frank, Nathaniel Echols, Jeffrey J. Headd, Thomas C. Terwilliger, Paul D. Adams and David Baker. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods (2013). DOI: 10.1038/nmeth.2648.
  47. Cherny, Izhack, Per Greisen, Yacov Ashani, Sagar D. Khare, Gustav Oberdorfer, Haim Leader, David Baker and Dan S. Tawfik. Engineering V-Type Nerve Agents Detoxifying Enzymes Using Computationally Focused Libraries. ACS Chemical Biology (2013). DOI: 10.1021/cb4004892.
  48. Song, Yifan, Frank DiMaio, Ray Yu-Ruei Wang, David Kim, Chris Miles, T. J. Brunette, James Thompson and David Baker. High-Resolution Comparative Modeling with RosettaCM. Structure (2013). DOI: 10.1016/j.str.2013.08.005.
  49. Adams, Paul D., David Baker, Axel T. Brunger et al. Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems. Annual Review of Biophysics (2013). DOI: 10.1146/annurev-biophys-083012-130253.
  50. Lange, Oliver F., Paolo Rossi, Nikolaos G. Sgourakis et al. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proceedings of the National Academy of Sciences (2012). DOI: 10.1073/pnas.1203013109.
  51. Azoitei, Mihai L., Yih-En Andrew Ban, Jean-Philippe Julien et al. Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope. Journal of Molecular Biology (2012). DOI: 10.1016/j.jmb.2011.10.003.
  52. Wodak, Shoshana J. Next-generation protein engineering targets influenza. Nature Biotechnology (2012). DOI: 10.1038/nbt.2268.
  53. Terwilliger, Thomas C., Frank DiMaio, Randy J. Read et al. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. Journal of Structural and Functional Genomics (2012). DOI: 10.1007/s10969-012-9129-3.
  54. Khare, Sagar D., Yakov Kipnis, Per Jr Greisen et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology (2012). DOI: 10.1038/nchembio.777.
  55. Tyka, Michael D., Kenneth Jung and David Baker. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. Journal of Computational Chemistry (2012). DOI: 10.1002/jcc.23069.
  56. King, Neil P., William Sheffler, Michael R. Sawaya et al. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy. Science (2012). DOI: 10.1126/science.1219364.
  57. Ulge, Umut Y., David A. Baker and Raymond J. Monnat. Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering. Nucleic Acids Research (2011). DOI: 10.1093/nar/gkr022.
  58. Li, Mi, Frank DiMaio, Dongwen Zhou, Alla Gustchina, Jacek Lubkowski, Zbigniew Dauter, David Baker and Alexander Wlodawer. Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature Structural & Molecular Biology (2011). DOI: 10.1038/nsmb.1964.
  59. Khersonsky, Olga, Daniela Röthlisberger, Andrew M. Wollacott et al. Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution. Journal of Molecular Biology (2011). DOI: 10.1016/j.jmb.2011.01.041.
  60. Leaver-Fay, Andrew, Michael Tyka, Steven M. Lewis et al. Rosetta3. Methods in Enzymology (2011).
  61. Windbichler, Nikolai, Miriam Menichelli, Philippos Aris Papathanos et al. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature (2011). DOI: 10.1038/nature09937.
  62. Sgourakis, Nikolaos G., Oliver F. Lange, Frank DiMaio et al. Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Journal of the American Chemical Society (2011). DOI: 10.1021/ja111318m.
  63. DiMaio, Frank, Thomas C. Terwilliger, Randy J. Read et al. Improved molecular replacement by density- and energy-guided protein structure optimization. Nature (2011). DOI: 10.1038/nature09964.
  64. Karanicolas, John, Jacob E. Corn, Irwin Chen et al. A De Novo Protein Binding Pair By Computational Design and Directed Evolution. Molecular Cell (2011). DOI: 10.1016/j.molcel.2011.03.010.
  65. Guenaga, Javier, Pia Dosenovic, Gilad Ofek, David Baker, William R. Schief, Peter D. Kwong, Gunilla B. Karlsson Hedestam and Richard T. Wyatt. Heterologous Epitope-Scaffold Prime∶Boosting Immuno-Focuses B Cell Responses to the HIV-1 gp41 2F5 Neutralization Determinant. PLOS ONE (2011). DOI: 10.1371/journal.pone.0016074.
  66. Kellogg, Elizabeth H., Andrew Leaver-Fay and David Baker. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins: Structure, Function, and Bioinformatics (2011). DOI: 10.1002/prot.22921.
  67. Tyka, Michael D., Daniel A. Keedy, Ingemar André, Frank DiMaio, Yifan Song, David C. Richardson, Jane S. Richardson and David Baker. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping. Journal of Molecular Biology (2011). DOI: 10.1016/j.jmb.2010.11.008.
  68. Chen, Dong-Hua, Matthew L. Baker, Corey F. Hryc et al. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proceedings of the National Academy of Sciences (2011). DOI: 10.1073/pnas.1015739108.
  69. Fleishman, Sarel J., Timothy A. Whitehead, Damian C. Ekiert, Cyrille Dreyfus, Jacob E. Corn, Eva-Maria Strauch, Ian A. Wilson and David Baker. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin. Science (2011). DOI: 10.1126/science.1202617.
  70. Fleishman, Sarel J., Sagar D. Khare, Nobuyasu Koga and David Baker. Restricted sidechain plasticity in the structures of native proteins and complexes: Restricted Sidechain Plasticity. Protein Science (2011). DOI: 10.1002/pro.604.
  71. Cooper, Seth, David Baker, Zoran Popović et al. The challenge of designing scientific discovery games. the Fifth International Conference (2010). DOI: 10.1145/1822348.1822354.
  72. Kiss, Gert, Daniela Röthlisberger, David Baker and K. N. Houk. Evaluation and ranking of enzyme designs. Protein Science (2010). DOI: 10.1002/pro.462.
  73. Sanowar, Sarah, Pragya Singh, Richard A. Pfuetzner et al. Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System. mBio (2010). DOI: 10.1128/mBio.00158-10.
  74. Raman, Srivatsan, Oliver F. Lange, Paolo Rossi et al. NMR Structure Determination for Larger Proteins Using Backbone-Only Data. Science (2010). DOI: 10.1126/science.1183649.
  75. Siegel, Justin B., Alexandre Zanghellini, Helena M. Lovick et al. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction. Science (2010). DOI: 10.1126/science.1190239.
  76. Ofek, Gilad, F. Javier Guenaga, William R. Schief, Jeff Skinner, David Baker, Richard Wyatt and Peter D. Kwong. Elicitation of structure-specific antibodies by epitope scaffolds. Proceedings of the National Academy of Sciences (2010). DOI: 10.1073/pnas.1004728107.
  77. Fleishman, Sarel J., Jacob E. Corn, Eva M. Strauch et al. Rosetta in CAPRI rounds 13-19: Rosetta in CAPRI Rounds 13-19. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22784.
  78. Weerapana, Eranthie, Chu Wang, Gabriel M. Simon et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature (2010). DOI: 10.1038/nature09472.
  79. Sheffler, William and David Baker. RosettaHoles2: A volumetric packing measure for protein structure refinement and validation: RosettaHoles2 for Protein Structure. Protein Science (2010). DOI: 10.1002/pro.458.
  80. Das, Rhiju, John Karanicolas and David Baker. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods (2010). DOI: 10.1038/nmeth.1433.
  81. Raman, Srivatsan, Yuanpeng J. Huang, Binchen Mao, Paolo Rossi, James M. Aramini, Gaohua Liu, Gaetano T. Montelione and David Baker. Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data. Journal of the American Chemical Society (2010). DOI: 10.1021/ja905934c.
  82. Ashworth, Justin, Gregory K. Taylor, James J. Havranek, S. Arshiya Quadri, Barry L. Stoddard and David Baker. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research (2010). DOI: 10.1093/nar/gkq283.
  83. Sampathkumar, Parthasarathy, Frances Lu, Xun Zhao et al. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution: Structure of a Putative Benzoate Specific Porin. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22829.
  84. Fowler, Douglas M., Carlos L. Araya, Sarel J. Fleishman, Elizabeth H. Kellogg, Jason J. Stephany, David Baker and Stanley Fields. High-resolution mapping of protein sequence-function relationships. Nature Methods (2010). DOI: 10.1038/nmeth.1492.
  85. Liu, Lingfeng, Paul Murphy, David Baker and Stefan Lutz. Computational design of orthogonal nucleoside kinases. Chem. Commun. (2010). DOI: 10.1039/C0CC02961K.
  86. Correia, Bruno E., Yih-En Andrew Ban, Margaret A. Holmes et al. Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope. Structure (2010). DOI: 10.1016/j.str.2010.06.010.
  87. Tang, Yuefeng, William M. Schneider, Yang Shen, Srivatsan Raman, Masayori Inouye, David Baker, Monica J. Roth and Gaetano T. Montelione. Fully automated high-quality NMR structure determination of small 2H-enriched proteins. Journal of Structural and Functional Genomics (2010). DOI: 10.1007/s10969-010-9095-6.
  88. Baker, David. An exciting but challenging road ahead for computational enzyme design. Protein Science (2010). DOI: 10.1002/pro.481.
  89. Wang, Chu, Robert Vernon, Oliver Lange, Michael Tyka and David Baker. Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry: Structure Prediction of Zinc-Binding Proteins. Protein Science (2010). DOI: 10.1002/pro.327.
  90. Blum, Ben, Michael I. Jordan and David Baker. Feature space resampling for protein conformational search. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22677.
  91. Thyme, Summer B., Jordan Jarjour, Ryo Takeuchi, James J. Havranek, Justin Ashworth, Andrew M. Scharenberg, Barry L. Stoddard and David Baker. Exploitation of binding energy for catalysis and design. Nature (2009). DOI: 10.1038/nature08508.
  92. Zhu, Jieqing, Bing-Hao Luo, Patrick Barth, Jack Schonbrun, David Baker and Timothy A. Springer. The Structure of a Receptor with Two Associating Transmembrane Domains on the Cell Surface: Integrin αIIbβ3. Molecular Cell (2009). DOI: 10.1016/j.molcel.2009.02.022.
  93. Das, Rhiju, Ingemar André, Yang Shen et al. Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America (2009). DOI: 10.1073/pnas.0904407106.
  94. Das, Rhiju and David Baker. Prospects for de novo phasing with de novo protein models. Acta Crystallographica Section D: Biological Crystallography (2009). DOI: 10.1107/S0907444908020039.
  95. Raman, Srivatsan, Robert Vernon, James Thompson et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22540.
  96. Sadreyev, R. I., S. Shi, D. Baker and N. V. Grishin. Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics (2009). DOI: 10.1093/bioinformatics/btp148.
  97. Ban, YA, BE Correia, M. Holmes et al. P05-09. 4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals. Retrovirology (2009). DOI: 10.1186/1742-4690-6-S3-P85.
  98. Davis, Ian W., Kaushik Raha, Martha S. Head and David Baker. Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Science (2009). DOI: 10.1002/pro.192.
  99. Barth, P., B. Wallner and D. Baker. Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences (2009). DOI: 10.1073/pnas.0808323106.
  100. Kidd, Brian A., David Baker and Wendy E. Thomas. Computation of Conformational Coupling in Allosteric Proteins. PLoS Computational Biology (2009). DOI: 10.1371/journal.pcbi.1000484.
  101. Shen, Yang, Robert Vernon, David Baker and Ad Bax. De novo protein structure generation from incomplete chemical shift assignments. Journal of Biomolecular NMR (2009). DOI: 10.1007/s10858-008-9288-5.
  102. Krieger, Elmar, Keehyoung Joo, Jinwoo Lee et al. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22570.
  103. Dietrich, Jeffrey A., Yasuo Yoshikuni, Karl J. Fisher et al. A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450BM3. ACS Chemical Biology (2009). DOI: 10.1021/cb900006h.
  104. Kim, David E., Ben Blum, Philip Bradley and David Baker. Sampling Bottlenecks in De novo Protein Structure Prediction. Journal of Molecular Biology (2009). DOI: 10.1016/j.jmb.2009.07.063.
  105. DiMaio, Frank, Michael D. Tyka, Matthew L. Baker, Wah Chiu and David Baker. Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta. Journal of Molecular Biology (2009). DOI: 10.1016/j.jmb.2009.07.008.
  106. Havranek, James J. and David Baker. Motif-directed flexible backbone design of functional interactions. Protein Science (2009). DOI: 10.1002/pro.142.
  107. Murphy, Paul M., Jill M. Bolduc, Jasmine L. Gallaher, Barry L. Stoddard and David Baker. Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences (2009). DOI: 10.1073/pnas.0811070106.
  108. Ashworth, Justin and David Baker. Assessment of the optimization of affinity and specificity at protein–DNA interfaces. Nucleic Acids Research (2009). DOI: 10.1093/nar/gkp242.
  109. Muratore, Kathryn E., Markus A. Seeliger, Zhihong Wang et al. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue. Biochemistry (2009). DOI: 10.1021/bi900057g.
  110. Luo, Bing-Hao, John Karanicolas, Laura D. Harmacek, David Baker and Timothy A. Springer. Rationally Designed Integrin β3 Mutants Stabilized in the High Affinity Conformation. Journal of Biological Chemistry (2009). DOI: 10.1074/jbc.M806312200.
  111. Rosato, Antonio, Anurag Bagaria, David Baker et al. CASD-NMR: critical assessment of automated structure determination by NMR. Nature Methods (2009). DOI: 10.1038/nmeth0909-625.
  112. Röthlisberger, Daniela, Olga Khersonsky, Andrew M. Wollacott et al. Kemp elimination catalysts by computational enzyme design. Nature (2008). DOI: 10.1038/nature06879.
  113. Das, Rhiju and David Baker. Macromolecular Modeling with Rosetta. Annual Review of Biochemistry (2008). DOI: 10.1146/annurev.biochem.77.062906.171838.
  114. Sheffler, Will and David Baker. RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design and validation. Protein Science (2008). DOI: 10.1002/pro.8.
  115. Fan, Erkang, David Baker, Stanley Fields et al. Structural Genomics of Pathogenic Protozoa: an Overview. Structural Proteomics (2008).
  116. Keeble, Anthony H., Lukasz A. Joachimiak, María Jesus Maté, Nicola Meenan, Nadine Kirkpatrick, David Baker and Colin Kleanthous. Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases. Journal of Molecular Biology (2008). DOI: 10.1016/j.jmb.2008.03.055.
  117. Alexandrova, Anastassia N., Daniela Röthlisberger, David Baker and William L. Jorgensen. Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination. Journal of the American Chemical Society (2008). DOI: 10.1021/ja804040s.
  118. McBeth, Christine, Audrey Seamons, Juan C. Pizarro, Sarel J. Fleishman, David Baker, Tanja Kortemme, Joan M. Goverman and Roland K. Strong. A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR. Journal of Molecular Biology (2008). DOI: https://doi.org/10.1016/j.jmb.2007.11.020.
  119. André, Ingemar, Charlie E. M. Strauss, David B. Kaplan, Philip Bradley and David Baker. Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences (2008). DOI: 10.1073/pnas.0807576105.
  120. Das, Rhiju, Madhuri Kudaravalli, Magdalena Jonikas et al. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America (2008). DOI: 10.1073/pnas.0709032105.
  121. Raman, S., B. Qian, D. Baker and R. C. Walker. Advances in Rosetta protein structure prediction on massively parallel systems. IBM Journal of Research and Development (2008). DOI: 10.1147/rd.521.0007.
  122. Shen, Yang, Oliver Lange, Frank Delaglio et al. Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America (2008). DOI: 10.1073/pnas.0800256105.
  123. Jiang, Lin, Eric A. Althoff, Fernando R. Clemente et al. De Novo Computational Design of Retro-Aldol Enzymes. Science (New York, N.Y.) (2008). DOI: 10.1126/science.1152692.
  124. Lengyel, Candice S.E., Lindsey J. Willis, Patrick Mann, David Baker, Tanja Kortemme, Roland K. Strong and Benjamin J. McFarland. Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity. Journal of Biological Chemistry (2007). DOI: 10.1074/jbc.M704513200.
  125. Qiu, Jian, Will Sheffler, David Baker and William Stafford Noble. Ranking predicted protein structures with support vector regression. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21809.
  126. André, Ingemar, Philip Bradley, Chu Wang and David Baker. Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0702626104.
  127. Malmström, Lars, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau and David Baker. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology (2007). DOI: 10.1371/journal.pbio.0050076.
  128. Kopp, Jürgen, Lorenza Bordoli, James N.D. Battey, Florian Kiefer and Torsten Schwede. Assessment of CASP7 predictions for template-based modeling targets. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21753.
  129. Stankunas, Kryn, J. Henri Bayle, James J. Havranek, Thomas J. Wandless, David Baker, Gerald R. Crabtree and Jason E. Gestwicki. Rescue of Degradation-Prone Mutants of the FK506-Rapamycin Binding (FRB) Protein with Chemical Ligands. ChemBioChem (2007). DOI: 10.1002/cbic.200700087.
  130. Jauch, Ralf, Hock Chuan Yeo, Prasanna R. Kolatkar and Neil D. Clarke. Assessment of CASP7 structure predictions for template free targets. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21771.
  131. Wojtowicz, Woj M., Wei Wu, Ingemar Andre, Bin Qian, David Baker and S. Lawrence Zipursky. A Vast Repertoire of Dscam Binding Specificities Arises from Modular Interactions of Variable Ig Domains. Cell (2007). DOI: 10.1016/j.cell.2007.08.026.
  132. Wollacott, Andrew M., Alexandre Zanghellini, Paul Murphy and David Baker. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Science: A Publication of the Protein Society (2007). DOI: 10.1110/ps.062270707.
  133. Knight, James D. R., Bin Qian, David Baker and Rashmi Kothary. Conservation, Variability and the Modeling of Active Protein Kinases. PLOS ONE (2007). DOI: 10.1371/journal.pone.0000982.
  134. Windbichler, Nikolai, Philippos Aris Papathanos, Flaminia Catteruccia, Hilary Ranson, Austin Burt and Andrea Crisanti. Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos. Nucleic Acids Research (2007). DOI: 10.1093/nar/gkm632.
  135. Wang, Chu, Ora Schueler-Furman, Ingemar Andre, Nir London, Sarel J. Fleishman, Philip Bradley, Bin Qian and David Baker. RosettaDock in CAPRI rounds 6-12. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21684.
  136. Tsemekhman, Kiril, Lukasz Goldschmidt, David Eisenberg and David Baker. Cooperative hydrogen bonding in amyloid formation. Protein Science (2007). DOI: 10.1110/ps.062609607.
  137. Dantas, Gautam, Colin Corrent, Steve L. Reichow et al. High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design. Journal of Molecular Biology (2007). DOI: 10.1016/j.jmb.2006.11.080.
  138. Barth, P., J. Schonbrun and D. Baker. Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0702515104.
  139. Goobes, Gil, Rivka Goobes, Wendy J. Shaw et al. The structure, dynamics, and energetics of protein adsorption—lessons learned from adsorption of statherin to hydroxyapatite. Magnetic Resonance in Chemistry (2007). DOI: 10.1002/mrc.2123.
  140. Watters, Alexander L., Pritilekha Deka, Colin Corrent, David Callender, Gabriele Varani, Tobin Sosnick and David Baker. The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection. Cell (2007). DOI: 10.1016/j.cell.2006.12.042.
  141. Shcherbata, Halyna R, Andriy S Yatsenko, Larissa Patterson, Vanita D Sood, Uri Nudel, David Yaffe, David Baker and Hannele Ruohola-Baker. Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO Journal (2007). DOI: 10.1038/sj.emboj.7601503.
  142. Tress, Michael, Jianlin Cheng, Pierre Baldi et al. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21675.
  143. Qian, Bin, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J. McCoy, Randy J. Read and David Baker. High-resolution structure prediction and the crystallographic phase problem. Nature (2007). DOI: 10.1038/nature06249.
  144. Wang, Chu, Philip Bradley and David Baker. Protein–Protein Docking with Backbone Flexibility. Journal of Molecular Biology (2007). DOI: 10.1016/j.jmb.2007.07.050.
  145. Das, Rhiju, Bin Qian, Srivatsan Raman et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007). DOI: 10.1002/prot.21636.
  146. Das, Rhiju and David Baker. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0703836104.
  147. Sood, Vanita D. and David Baker. Recapitulation and Design of Protein Binding Peptide Structures and Sequences. Journal of Molecular Biology (2006). DOI: 10.1016/j.jmb.2006.01.045.
  148. Thompson, Michael J., Stuart A. Sievers, John Karanicolas, Magdalena I. Ivanova, David Baker and David Eisenberg. The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences (2006). DOI: 10.1073/pnas.0511295103.
  149. Sprague, Elizabeth R., Chu Wang, David Baker and Pamela J. Bjorkman. Crystal Structure of the HSV-1 Fc Receptor Bound to Fc Reveals a Mechanism for Antibody Bipolar Bridging. PLOS Biology (2006). DOI: 10.1371/journal.pbio.0040148.
  150. Baker, Matthew L., Wen Jiang, William J. Wedemeyer, Frazer J. Rixon, David Baker and Wah Chiu. Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density. PLOS Computational Biology (2006). DOI: 10.1371/journal.pcbi.0020146.
  151. Dantas, Gautam, Alexander L. Watters, Bradley M. Lunde et al. Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution. Journal of Molecular Biology (2006). DOI: 10.1016/j.jmb.2006.07.092.
  152. Goobes, Gil, Rivka Goobes, Ora Schueler-Furman, David Baker, Patrick S. Stayton and Gary P. Drobny. Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences (2006). DOI: 10.1073/pnas.0607193103.
  153. Palmer, Amy E., Marta Giacomello, Tanja Kortemme, S. Andrew Hires, Varda Lev-Ram, David Baker and Roger Y. Tsien. Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs. Chemistry & Biology (2006). DOI: 10.1016/j.chembiol.2006.03.007.
  154. Yarov-Yarovoy, Vladimir, Jack Schonbrun and David Baker. Multipass membrane protein structure prediction using Rosetta. Proteins (2006). DOI: 10.1002/prot.20817.
  155. Dobson, Neil, Gautam Dantas, David Baker and Gabriele Varani. High-Resolution Structural Validation of the Computational Redesign of Human U1A Protein. Structure (2006). DOI: 10.1016/j.str.2006.02.011.
  156. Chivian, Dylan and David Baker. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Research (2006). DOI: 10.1093/nar/gkl480.
  157. Bradley, Philip and David Baker. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins: Structure, Function, and Bioinformatics (2006). DOI: 10.1002/prot.21133.
  158. Morozov, Alexandre V., Kiril Tsemekhman and David Baker. Electron Density Redistribution Accounts for Half the Cooperativity of α Helix Formation. The Journal of Physical Chemistry B (2006). DOI: 10.1021/jp057161f.
  159. Misura, Kira M. S., Dylan Chivian, Carol A. Rohl, David E. Kim and David Baker. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America (2006). DOI: 10.1073/pnas.0509355103.
  160. Baker, David. Prediction and design of macromolecular structures and interactions. Philosophical Transactions of the Royal Society B: Biological Sciences (2006). DOI: 10.1098/rstb.2005.1803.
  161. Meiler, Jens and David Baker. ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility. Proteins: Structure, Function, and Bioinformatics (2006). DOI: 10.1002/prot.21086.
  162. Yarov-Yarovoy, Vladimir, David Baker and William A. Catterall. Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proceedings of the National Academy of Sciences of the United States of America (2006). DOI: 10.1073/pnas.0602350103.
  163. Ashworth, Justin, James J. Havranek, Carlos M. Duarte, Django Sussman, Raymond J. Monnat, Barry L. Stoddard and David Baker. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006). DOI: 10.1038/nature04818.
  164. Zanghellini, Alexandre, Lin Jiang, Andrew M. Wollacott, Gong Cheng, Jens Meiler, Eric A. Althoff, Daniela Röthlisberger and David Baker. New algorithms and an in silico benchmark for computational enzyme design. Protein Science (2006). DOI: 10.1110/ps.062353106.
  165. Joachimiak, Lukasz A., Tanja Kortemme, Barry L. Stoddard and David Baker. Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface. Journal of Molecular Biology (2006). DOI: 10.1016/j.jmb.2006.05.022.
  166. Daily, Michael D., David Masica, Arvind Sivasubramanian, Sony Somarouthu and Jeffrey J. Gray. CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20555.
  167. Meiler, Jens and David Baker. The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of Magnetic Resonance (2005). DOI: 10.1016/j.jmr.2004.11.031.
  168. Bradley, Philip, Kira M. S. Misura and David Baker. Toward High-Resolution de Novo Structure Prediction for Small Proteins. Science (2005). DOI: 10.1126/science.1113801.
  169. Morozov, A. V. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research (2005). DOI: 10.1093/nar/gki875.
  170. Schueler-Furman, Ora, Chu Wang, Phil Bradley, Kira Misura and David Baker. Progress in Modeling of Protein Structures and Interactions. Science (2005). DOI: 10.1126/science.1112160.
  171. Schueler-Furman, Ora, Chu Wang and David Baker. Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20556.
  172. Cheng, Gong, Bin Qian, Ram Samudrala and David Baker. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research (2005). DOI: 10.1093/nar/gki894.
  173. Saunders, Christopher T. and David Baker. Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design. Journal of Molecular Biology (2005). DOI: 10.1016/j.jmb.2004.11.062.
  174. Wang, Chu, Ora Schueler-Furman and David Baker. Improved side-chain modeling for protein–protein docking. Protein Science (2005). DOI: 10.1110/ps.041222905.
  175. Bradley, Philip, Lars Malmström, Bin Qian et al. Free modeling with Rosetta in CASP6. Proteins (2005). DOI: 10.1002/prot.20729.
  176. Graña, Osvaldo, David Baker, Robert M. MacCallum, Jens Meiler, Marco Punta, Burkhard Rost, Michael L. Tress and Alfonso Valencia. CASP6 assessment of contact prediction. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20739.
  177. Korkegian, Aaron, Margaret E. Black, David Baker and Barry L. Stoddard. Computational Thermostabilization of an Enzyme. Science (2005). DOI: 10.1126/science.1107387.
  178. Chivian, Dylan, David E. Kim, Lars Malmström, Jack Schonbrun, Carol A. Rohl and David Baker. Prediction of CASP6 structures using automated Robetta protocols. Proteins (2005). DOI: 10.1002/prot.20733.
  179. Lacy, D. Borden, Henry C. Lin, Roman A. Melnyk, Ora Schueler-Furman, Laura Reither, Kristina Cunningham, David Baker and R. John Collier. A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America (2005). DOI: 10.1073/pnas.0508259102.
  180. Misura, Kira M.S. and David Baker. Progress and challenges in high-resolution refinement of protein structure models. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20376.


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