synergy logo 3
BOINC Synergy

Rosetta@home

Rosetta@home Logo

Rosetta@home is a volunteer distributed computing project that uses BOINC and needs your help to speed up and extend our efforts to design new proteins and to predict their 3-dimensional shapes.

Why Rosetta@home?

Help efforts at designing new proteins to fight diseases such as COVID-19, HIV, malaria, cancer, and Alzheimer's.

Goal

Determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases.

Methods

Speed up and extend research in ways we couldn't possibly attempt without the help of volunteer computing.

Project team / Sponsors

https://www.bakerlab.org

Scientific publications

Source: https://boinc.berkeley.edu/pubs.php#Rosetta@home


  1. Zhou, Guangfeng, Domnita-Valeria Rusnac, Hahnbeom Park et al. An artificial intelligence accelerated virtual screening platform for drug discovery. Nature Communications (2024). DOI: 10.1038/s41467-024-52061-7.
  2. Salveson, Patrick J., Adam P. Moyer, Meerit Y. Said et al. Expansive discovery of chemically diverse structured macrocyclic oligoamides. Science (2024). DOI: 10.1126/science.adk1687.
  3. Goverde, Casper A., Martin Pacesa, Nicolas Goldbach et al. Computational design of soluble and functional membrane protein analogues. Nature (2024). DOI: 10.1038/s41586-024-07601-y.
  4. Sun, Ke, Sicong Li, Bowen Zheng et al. Accurate de novo design of heterochiral protein–protein interactions. Cell Research (2024). DOI: 10.1038/s41422-024-01014-2.
  5. Baryshev, Alexandr, Alyssa La Fleur, Benjamin Groves, Cirstyn Michel, David Baker, Ajasja Ljubetič and Georg Seelig. Massively parallel measurement of protein–protein interactions by sequencing using MP3-seq. Nature Chemical Biology (2024). DOI: 10.1038/s41589-024-01718-x.
  6. Sumida, Kiera H., Reyes Núñez-Franco, Indrek Kalvet et al. Improving Protein Expression, Stability, and Function with ProteinMPNN. Journal of the American Chemical Society (2024). DOI: 10.1021/jacs.3c10941.
  7. Zhang, Jason Z., William H. Nguyen, Nathan Greenwood, John C. Rose, Shao-En Ong, Dustin J. Maly and David Baker. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nature Biotechnology (2024). DOI: 10.1038/s41587-023-02107-w.
  8. Mout, Rubul, Ross C. Bretherton, Justin Decarreau et al. De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity. Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2309457121.
  9. Krishna, Rohith, Jue Wang, Woody Ahern et al. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (2024). DOI: 10.1126/science.adl2528.
  10. Huddy, Timothy F., Yang Hsia, Ryan D. Kibler et al. Blueprinting extendable nanomaterials with standardized protein blocks. Nature (2024). DOI: 10.1038/s41586-024-07188-4.
  11. Sahtoe, Danny D., Ewa A. Andrzejewska, Hannah L. Han et al. Design of amyloidogenic peptide traps. Nature Chemical Biology (2024). DOI: 10.1038/s41589-024-01578-5.
  12. Mansoor, Sanaa, Minkyung Baek, Hahnbeom Park, Gyu Rie Lee and David Baker. Protein Ensemble Generation Through Variational Autoencoder Latent Space Sampling. Journal of Chemical Theory and Computation (2024). DOI: 10.1021/acs.jctc.3c01057.
  13. Shen, Hao, Eric M. Lynch, Susrut Akkineni et al. De novo design of pH-responsive self-assembling helical protein filaments. Nature Nanotechnology (2024). DOI: 10.1038/s41565-024-01641-1.
  14. Craven, Timothy W., Mark D. Nolan, Jonathan Bailey et al. Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase. ACS Chemical Biology (2024). DOI: 10.1021/acschembio.4c00076.
  15. Vázquez Torres, Susana, Philip J. Y. Leung, Preetham Venkatesh et al. De novo design of high-affinity binders of bioactive helical peptides. Nature (2024). DOI: 10.1038/s41586-023-06953-1.
  16. Yang, Erin C., Robby Divine, Marcos C. Miranda et al. Computational design of non-porous pH-responsive antibody nanoparticles. Nature Structural & Molecular Biology (2024). DOI: 10.1038/s41594-024-01288-5.
  17. Jiang, Hanlun, Kevin M. Jude, Kejia Wu et al. De novo design of buttressed loops for sculpting protein functions. Nature Chemical Biology (2024). DOI: 10.1038/s41589-024-01632-2.
  18. Edman, Natasha I., Ashish Phal, Rachel L. Redler et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell (2024). DOI: 10.1016/j.cell.2024.05.025.
  19. Berger, Stephanie, Franziska Seeger, Ta-Yi Yu et al. Preclinical proof of principle for orally delivered Th17 antagonist miniproteins. Cell (2024). DOI: 10.1016/j.cell.2024.05.052.
  20. Pillai, Arvind, Abbas Idris, Annika Philomin et al. De novo design of allosterically switchable protein assemblies. Nature (2024). DOI: 10.1038/s41586-024-07813-2.
  21. Huang, Buwei, Brian Coventry, Marta T. Borowska et al. De novo design of miniprotein antagonists of cytokine storm inducers. Nature Communications (2024). DOI: 10.1038/s41467-024-50919-4.
  22. Humphreys, Ian R., Jing Zhang, Minkyung Baek et al. Protein interactions in human pathogens revealed through deep learning. Nature Microbiology (2024). DOI: 10.1038/s41564-024-01791-x.
  23. Lisanza, Sidney Lyayuga, Jacob Merle Gershon, Samuel W. K. Tipps et al. Multistate and functional protein design using RoseTTAFold sequence space diffusion. Nature Biotechnology (2024). DOI: 10.1038/s41587-024-02395-w.
  24. Huang, Buwei, Mohamad Abedi, Green Ahn et al. Designed endocytosis-inducing proteins degrade targets and amplify signals. Nature (2024). DOI: 10.1038/s41586-024-07948-2.
  25. Kibler, Ryan D., Sangmin Lee, Madison A. Kennedy et al. Design of pseudosymmetric protein hetero-oligomers. Nature Communications (2024). DOI: 10.1038/s41467-024-54913-8.
  26. Dowling, Quinton M., Young-Jun Park, Chelsea N. Fries et al. Hierarchical design of pseudosymmetric protein nanocages. Nature (2024). DOI: 10.1038/s41586-024-08360-6.
  27. Baek, Minkyung, Ryan McHugh, Ivan Anishchenko, Hanlun Jiang, David Baker and Frank DiMaio. Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA. Nature Methods (2024). DOI: 10.1038/s41592-023-02086-5.
  28. Muratspahić, Edin, Kristine Deibler, Jianming Han et al. Design and structural validation of peptide–drug conjugate ligands of the kappa-opioid receptor. Nature Communications (2023). DOI: 10.1038/s41467-023-43718-w.
  29. Davila-Hernandez, Fatima A., Biao Jin, Harley Pyles et al. Directing polymorph specific calcium carbonate formation with de novo protein templates. Nature Communications (2023). DOI: 10.1038/s41467-023-43608-1.
  30. Kalvet, Indrek, Mary Ortmayer, Jingming Zhao et al. Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site. Journal of the American Chemical Society (2023). DOI: 10.1021/jacs.3c02742.
  31. Gerben, Stacey R, Andrew J Borst, Derrick R Hicks et al. Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins. Biochemistry (2023). DOI: 10.1021/acs.biochem.2c00497.
  32. Motmaen, Amir, Justas Dauparas, Minkyung Baek, Mohamad H. Abedi, David Baker and Philip Bradley. Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2216697120.
  33. Yeh, Andy Hsien-Wei, Christoffer Norn, Yakov Kipnis et al. De novo design of luciferases using deep learning. Nature (2023). DOI: 10.1038/s41586-023-05696-3.
  34. Rettie, Stephen A., Katelyn V. Campbell, Asim K. Bera et al. Cyclic peptide structure prediction and design using AlphaFold. (2023).
  35. Wu, Kejia, Hua Bai, Ya-Ting Chang et al. De novo design of modular peptide-binding proteins by superhelical matching. Nature (2023). DOI: 10.1038/s41586-023-05909-9.
  36. Lutz, Isaac D., Shunzhi Wang, Christoffer Norn et al. Top-down design of protein architectures with reinforcement learning. Science (2023). DOI: 10.1126/science.adf6591.
  37. Kim, David E., Davin R. Jensen, David Feldman et al. De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2207974120.
  38. Watson, Joseph L., David Juergens, Nathaniel R. Bennett et al. De novo design of protein structure and function with RFdiffusion. Nature (2023). DOI: 10.1038/s41586-023-06415-8.
  39. Goldbach, Nicolas, Issa Benna, Basile I. M. Wicky et al. De novo design of monomeric helical bundles for pH-controlled membrane lysis. Protein Science (2023). DOI: 10.1002/pro.4769.
  40. Bethel, Neville P., Andrew J. Borst, Fabio Parmeggiani et al. Precisely patterned nanofibres made from extendable protein multiplexes. Nature Chemistry (2023). DOI: 10.1038/s41557-023-01314-x.
  41. Mansoor, Sanaa, Minkyung Baek, David Juergens, Joseph L. Watson and David Baker. Zero-shot mutation effect prediction on protein stability and function using RoseTTAFold. Protein Science (2023). DOI: 10.1002/pro.4780.
  42. Roy, Anindya, Lei Shi, Ashley Chang et al. De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Nature Communications (2023). DOI: 10.1038/s41467-023-41272-z.
  43. An, Linna, Derrick R. Hicks, Dmitri Zorine et al. Hallucination of closed repeat proteins containing central pockets. Nature Structural & Molecular Biology (2023). DOI: 10.1038/s41594-023-01112-6.
  44. Li, Zhe, Shunzhi Wang, Una Nattermann et al. Accurate computational design of three-dimensional protein crystals. Nature Materials (2023). DOI: 10.1038/s41563-023-01683-1.
  45. Praetorius, Florian, Philip J. Y. Leung, Maxx H. Tessmer et al. Design of stimulus-responsive two-state hinge proteins. Science (2023). DOI: 10.1126/science.adg7731.
  46. Wang, Jue, Sidney Lisanza, David Juergens et al. Scaffolding protein functional sites using deep learning. Science (2022). DOI: 10.1126/science.abn2100.
  47. Cao, Longxing, Brian Coventry, Inna Goreshnik et al. Design of protein-binding proteins from the target structure alone. Nature (2022). DOI: 10.1038/s41586-022-04654-9.
  48. Baek, Minkyung and David Baker. Deep learning and protein structure modeling. Nature Methods (2022). DOI: 10.1038/s41592-021-01360-8.
  49. Sahtoe, Danny D., Florian Praetorius, Alexis Courbet et al. Reconfigurable asymmetric protein assemblies through implicit negative design. Science (2022). DOI: 10.1126/science.abj7662.
  50. Kipnis, Yakov, Anissa Ouald Chaib, Anastassia A. Vorobieva et al. Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Protein Science (2022). DOI: 10.1002/pro.4405.
  51. Hicks, Derrick R., Madison A. Kennedy, Kirsten A. Thompson et al. De novo design of protein homodimers containing tunable symmetric protein pockets. Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2113400119.
  52. Bhardwaj, Gaurav, Jacob O’Connor, Stephen Rettie et al. Accurate de novo design of membrane-traversing macrocycles. Cell (2022). DOI: 10.1016/j.cell.2022.07.019.
  53. Said, Meerit Y., Christine S. Kang, Shunzhi Wang et al. Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks. Chemistry of Materials (2022). DOI: 10.1021/acs.chemmater.2c02597.
  54. Bermeo, Sherry, Andrew Favor, Ya-Ting Chang et al. De novo design of obligate ABC-type heterotrimeric proteins. Nature Structural & Molecular Biology (2022). DOI: 10.1038/s41594-022-00879-4.
  55. Courbet, A., J. Hansen, Y. Hsia et al. Computational design of mechanically coupled axle-rotor protein assemblies. Science (2022). DOI: 10.1126/science.abm1183.
  56. Hunt, Andrew C., James Brett Case, Young-Jun Park et al. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Science Translational Medicine (2022). DOI: 10.1126/scitranslmed.abn1252.
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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.
  67. 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.
  68. 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.
  69. Cong, Qian, Ivan Anishchenko, Sergey Ovchinnikov and David Baker. Protein interaction networks revealed by proteome coevolution. Science (2019). DOI: 10.1126/science.aaw6718.
  70. 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.
  71. 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.
  72. 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.
  73. 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.
  74. Lu, Peilong, Duyoung Min, Frank DiMaio et al. Accurate computational design of multipass transmembrane proteins. Science (2018). DOI: 10.1126/science.aaq1739.
  75. 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.
  76. Hosseinzadeh, Parisa, Gaurav Bhardwaj, Vikram Khipple Mulligan et al. Comprehensive computational design of ordered peptide macrocycles. Science (2017). DOI: 10.1126/science.aap7577.
  77. Ovchinnikov, Sergey, Hahnbeom Park, Neha Varghese et al. Protein structure determination using metagenome sequence data. Science (2017). DOI: 10.1126/science.aah4043.
  78. 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.
  79. Bhardwaj, Gaurav, Vikram Khipple Mulligan, Christopher D. Bahl et al. Accurate de novo design of hyperstable constrained peptides. Nature (2016). DOI: 10.1038/nature19791.
  80. 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.
  81. Hsia, Yang, Jacob B. Bale, Shane Gonen et al. Design of a hyperstable 60-subunit protein icosahedron. Nature (2016). DOI: 10.1038/nature18010.
  82. 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.
  83. 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.
  84. 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.
  85. 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.
  86. 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.
  87. 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.
  88. 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.
  89. 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.
  90. 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.
  91. 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.
  92. Baker, David. Protein folding, structure prediction and design. Biochemical Society Transactions (2014). DOI: 10.1042/BST20130055.
  93. 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.
  94. 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.
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. Huang, Po-Ssu, Gustav Oberdorfer, Chunfu Xu et al. High thermodynamic stability of parametrically designed helical bundles. Science (2014). DOI: 10.1126/science.1257481.
  100. 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.
  101. 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.
  102. 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.
  103. 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.
  104. 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.
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. 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.
  110. Wodak, Shoshana J. Next-generation protein engineering targets influenza. Nature Biotechnology (2012). DOI: 10.1038/nbt.2268.
  111. 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.
  112. 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.
  113. 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.
  114. 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.
  115. Leaver-Fay, Andrew, Michael Tyka, Steven M. Lewis et al. Rosetta3. Methods in Enzymology (2011).
  116. 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.
  117. 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.
  118. 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.
  119. 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.
  120. 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.
  121. 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.
  122. 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.
  123. 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.
  124. 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.
  125. 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.
  126. 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.
  127. 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.
  128. 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.
  129. 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.
  130. 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.
  131. Baker, David. An exciting but challenging road ahead for computational enzyme design. Protein Science (2010). DOI: 10.1002/pro.481.
  132. 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.
  133. 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.
  134. 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.
  135. Das, Rhiju, John Karanicolas and David Baker. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods (2010). DOI: 10.1038/nmeth.1433.
  136. 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.
  137. 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.
  138. 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.
  139. Kiss, Gert, Daniela Röthlisberger, David Baker and K. N. Houk. Evaluation and ranking of enzyme designs. Protein Science (2010). DOI: 10.1002/pro.462.
  140. Liu, Lingfeng, Paul Murphy, David Baker and Stefan Lutz. Computational design of orthogonal nucleoside kinases. Chem. Commun. (2010). DOI: 10.1039/C0CC02961K.
  141. 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.
  142. 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.
  143. Weerapana, Eranthie, Chu Wang, Gabriel M. Simon et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature (2010). DOI: 10.1038/nature09472.
  144. 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.
  145. 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.
  146. Muratore, Kathryn E., Markus A. Seeliger, Zhihong Wang et al. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue. Biochemistry (2009). DOI: 10.1021/bi900057g.
  147. 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.
  148. 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.
  149. 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.
  150. 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.
  151. 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.
  152. 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.
  153. 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.
  154. 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.
  155. 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.
  156. 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.
  157. 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.
  158. 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.
  159. 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.
  160. 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.
  161. 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.
  162. Havranek, James J. and David Baker. Motif-directed flexible backbone design of functional interactions. Protein Science (2009). DOI: 10.1002/pro.142.
  163. 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.
  164. 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.
  165. 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.
  166. 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.
  167. 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.
  168. Fan, Erkang, David Baker, Stanley Fields et al. Structural Genomics of Pathogenic Protozoa: an Overview. Structural Proteomics (2008).
  169. 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.
  170. 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.
  171. 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.
  172. 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.
  173. Röthlisberger, Daniela, Olga Khersonsky, Andrew M. Wollacott et al. Kemp elimination catalysts by computational enzyme design. Nature (2008). DOI: 10.1038/nature06879.
  174. Das, Rhiju and David Baker. Macromolecular Modeling with Rosetta. Annual Review of Biochemistry (2008). DOI: 10.1146/annurev.biochem.77.062906.171838.
  175. 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.
  176. 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.
  177. 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.
  178. 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.
  179. 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.
  180. 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.
  181. 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.
  182. 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.
  183. Tsemekhman, Kiril, Lukasz Goldschmidt, David Eisenberg and David Baker. Cooperative hydrogen bonding in amyloid formation. Protein Science (2007). DOI: 10.1110/ps.062609607.
  184. 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.
  185. 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.
  186. 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.
  187. 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.
  188. 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.
  189. 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.
  190. 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.
  191. 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.
  192. 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.
  193. 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.
  194. 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.
  195. 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.
  196. 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.
  197. 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.
  198. 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.
  199. Ozer, Stuart, David Kim and David Baker. Reporting@Home: Delivering Dynamic Graphical Feedback to Participants and Researchers in Community Computing Projects. (2007).
  200. 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.
  201. Yarov-Yarovoy, Vladimir, Jack Schonbrun and David Baker. Multipass membrane protein structure prediction using Rosetta. Proteins (2006). DOI: 10.1002/prot.20817.
  202. 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.
  203. 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.
  204. 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.
  205. 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.
  206. 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.
  207. 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.
  208. 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.
  209. 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.
  210. 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.
  211. 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.
  212. 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.
  213. 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.
  214. 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.
  215. 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.
  216. 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.
  217. 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.
  218. 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.
  219. 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.
  220. Bradley, Philip, Lars Malmström, Bin Qian et al. Free modeling with Rosetta in CASP6. Proteins (2005). DOI: 10.1002/prot.20729.
  221. 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.
  222. 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.
  223. Korkegian, Aaron, Margaret E. Black, David Baker and Barry L. Stoddard. Computational Thermostabilization of an Enzyme. Science (2005). DOI: 10.1126/science.1107387.
  224. 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.
  225. 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.
  226. 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.
  227. 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.
  228. 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.
  229. 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.
  230. 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.
  231. 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.
  232. Wang, Chu, Ora Schueler-Furman and David Baker. Improved side-chain modeling for protein–protein docking. Protein Science (2005). DOI: 10.1110/ps.041222905.
  233. Morozov, A. V. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research (2005). DOI: 10.1093/nar/gki875.
  234. 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.

Project Summary

This BOINC project enables volunteers to contribute computing power to scientific research from home. Results support breakthroughs in the respective field of study and demonstrate the potential of distributed computing.

Contributing

To participate, download and install BOINC and attach to the project using its official URL: https://boinc.bakerlab.org/rosetta/. Your computer will perform calculations and report results back to the project servers automatically.

Back to BOINC Wiki Home