Standout Papers

Protein structure prediction and analysis using the Robetta server 1998 2026 2007 2016 1.6k
  1. Protein structure prediction and analysis using the Robetta server (2004)
    David E. Kim, Dylan Chivian et al. Nucleic Acids Research
  2. Quantitative reactivity profiling predicts functional cysteines in proteomes (2010)
    Eranthie Weerapana, Chu Wang et al. Nature
  3. Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright (1998)
    Kevin W. Plaxco, Kim T. Simons et al. Journal of Molecular Biology
  4. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy (2003)
    Brian Kuhlman, Gautam Dantas et al. Science
  5. Protein Structure Prediction Using Rosetta (2004)
    Carol A. Rohl, Charlie E. M. Strauss et al. Methods in enzymology on CD-ROM/Methods in enzymology
  6. Protein Structure Prediction and Structural Genomics (2001)
    David Baker, Andrej Săli Science
  7. Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 (2009)
    Elmar Krieger, Keehyoung Joo et al. Proteins Structure Function and Bioinformatics
  8. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions (1997)
    Kim T. Simons, Charles Kooperberg et al. Journal of Molecular Biology
  9. The coming of age of de novo protein design (2016)
    Po‐Ssu Huang, Scott E. Boyken et al. Nature
  10. Kemp elimination catalysts by computational enzyme design (2008)
    Daniela Röthlisberger, Olga Khersonsky et al. Nature
  11. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design (2017)
    Rebecca F. Alford, Andrew Leaver‐Fay et al. Journal of Chemical Theory and Computation
  12. Improved protein structure prediction using predicted interresidue orientations (2020)
    Jianyi Yang, Ivan Anishchenko et al. Proceedings of the National Academy of Sciences
  13. De Novo Computational Design of Retro-Aldol Enzymes (2008)
    Lin Jiang, Eric A. Althoff et al. Science
  14. Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations (2003)
    Jeffrey J. Gray, Stewart Moughon et al. Journal of Molecular Biology
  15. High-Resolution Comparative Modeling with RosettaCM (2013)
    Yifan Song, Frank DiMaio et al. Structure
  16. Macromolecular Modeling with Rosetta (2008)
    Rhiju Das, David Baker Annual Review of Biochemistry
  17. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction (2010)
    Justin B. Siegel, Alexandre Zanghellini et al. Science
  18. Predicting protein structures with a multiplayer online game (2010)
    Seth Cooper, Firas Khatib et al. Nature
  19. Consistent blind protein structure generation from NMR chemical shift data (2008)
    Yang Shen, Oliver F. Lange et al. Proceedings of the National Academy of Sciences
  20. Native protein sequences are close to optimal for their structures (2000)
    Brian Kuhlman, David Baker Proceedings of the National Academy of Sciences
  21. A simple physical model for binding energy hot spots in protein–protein complexes (2002)
    Tanja Kortemme, David Baker Proceedings of the National Academy of Sciences
  22. Toward High-Resolution de Novo Structure Prediction for Small Proteins (2005)
    Philip Bradley, Kira M.S. Misura et al. Science
  23. A surprising simplicity to protein folding (2000)
    David Baker Nature
  24. An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae (2012)
    Adam J. Wargacki, Effendi Leonard et al. Science
  25. Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors (2013)
    Joseph G. Jardine, Jean‐Philippe Julien et al. Science
  26. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy (2012)
    Neil P. King, William Sheffler et al. Science
  27. High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis (2014)
    Gregory M. Alushin, Gabriel C. Lander et al. Cell
  28. Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era (2013)
    Hetunandan Kamisetty, Sergey Ovchinnikov et al. Proceedings of the National Academy of Sciences
  29. Role of conformational sampling in computing mutation‐induced changes in protein structure and stability (2010)
    Elizabeth H. Kellogg, Andrew Leaver‐Fay et al. Proteins Structure Function and Bioinformatics
  30. Computational Alanine Scanning of Protein-Protein Interfaces (2004)
    Tanja Kortemme, David E. Kim et al. Science s STKE
  31. Accurate design of co-assembling multi-component protein nanomaterials (2014)
    Neil P. King, Jacob B. Bale et al. Nature
  32. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014)
    Sergey Ovchinnikov, Hetunandan Kamisetty et al. eLife
  33. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin (2011)
    Sarel J. Fleishman, Timothy A. Whitehead et al. Science
  34. RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite (2011)
    Sarel J. Fleishman, Andrew Leaver‐Fay et al. PLoS ONE
  35. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors (2020)
    Longxing Cao, Inna Goreshnik et al. Science
  36. Plasma β-amyloid in Alzheimer’s disease and vascular disease (2016)
    Shorena Janelidze, Erik Stomrud et al. Scientific Reports
  37. An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes (2003)
    Tanja Kortemme, Alexandre V. Morozov et al. Journal of Molecular Biology
  38. Accurate design of megadalton-scale two-component icosahedral protein complexes (2016)
    Jacob B. Bale, Shane Gonen et al. Science
  39. Principles for designing ideal protein structures (2012)
    Nobuyasu Koga, Rie Koga et al. Nature
  40. The trRosetta server for fast and accurate protein structure prediction (2021)
    Zongyang Du, Hong Su et al. Nature Protocols
  41. Ab initio protein structure prediction of CASP III targets using ROSETTA (1999)
    Kim T. Simons, Ingo Ruczinski et al. Proteins Structure Function and Bioinformatics
  42. Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs (2006)
    Amy E. Palmer, Marta Giacomello et al. Chemistry & Biology
  43. Computational Enzyme Design (2013)
    Gert Kiss, Nihan Çelebi‐Ölçüm et al. Angewandte Chemie International Edition
  44. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation (2011)
    Stuart A. Sievers, John Karanicolas et al. Nature
  45. Mechanisms of protein folding (2001)
    Viara Grantcharova, Eric J. Alm et al. Current Opinion in Structural Biology
  46. High-resolution mapping of protein sequence-function relationships (2010)
    Douglas M. Fowler, Carlos L. Araya et al. Nature Methods
  47. Structure prediction for CASP8 with all‐atom refinement using Rosetta (2009)
    Srivatsan Raman, Robert M. Vernon et al. Proteins Structure Function and Bioinformatics
  48. Plasma tau in Alzheimer disease (2016)
    Niklas Mattsson, Henrik Zetterberg et al. Neurology
  49. ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility (2006)
    Jens Meiler, David Baker Proteins Structure Function and Bioinformatics
  50. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins (1999)
    Kim T. Simons, Ingo Ruczinski et al. Proteins Structure Function and Bioinformatics
  51. Protein structure determination using metagenome sequence data (2017)
    Sergey Ovchinnikov, Hahnbeom Park et al. Science
  52. Protein–Protein Docking with Backbone Flexibility (2007)
    Chu Wang, Philip Bradley et al. Journal of Molecular Biology
  53. Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila (1991)
    H Ruohola, K. Bremer et al. Cell
  54. The 3D profile method for identifying fibril-forming segments of proteins (2006)
    Michael J. Thompson, Stuart A. Sievers et al. Proceedings of the National Academy of Sciences
  55. Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules (2016)
    Hahnbeom Park, Philip Bradley et al. Journal of Chemical Theory and Computation
  56. Experiment and theory highlight role of native state topology in SH3 folding. (1999)
    David Baker, David S. Riddle et al. Nature Structural Biology
  57. Automated de novo prediction of native-like RNA tertiary structures (2007)
    Rhiju Das, David Baker Proceedings of the National Academy of Sciences
  58. Algorithm discovery by protein folding game players (2011)
    Firas Khatib, Seth Cooper et al. Proceedings of the National Academy of Sciences
  59. RosettaLigand Docking with Full Ligand and Receptor Flexibility (2008)
    Ian Davis, David Baker Journal of Molecular Biology
  60. Computational design of ligand-binding proteins with high affinity and selectivity (2013)
    Christine E. Tinberg, Sagar D. Khare et al. Nature
  61. Design of a hyperstable 60-subunit protein icosahedron (2016)
    Yang Hsia, Jacob B. Bale et al. Nature
  62. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures (1999)
    Eric J. Alm, David Baker Proceedings of the National Academy of Sciences
  63. De novo protein design by deep network hallucination (2021)
    Ivan Anishchenko, Samuel J. Pellock et al. Nature
  64. Computational protein design enables a novel one-carbon assimilation pathway (2015)
    Justin B. Siegel, Sean Poust et al. Proceedings of the National Academy of Sciences
  65. Global analysis of protein folding using massively parallel design, synthesis, and testing (2017)
    Sugyan M. Dixit, Tamuka M. Chidyausiku et al. Science
  66. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing (2012)
    Timothy A. Whitehead, Aaron Chevalier et al. Nature Biotechnology
  67. Reconstitution of SEC gene product-dependent intercompartmental protein transport (1988)
    David Baker, Linda Hicke et al. Cell
  68. Relaxation of backbone bond geometry improves protein energy landscape modeling (2013)
    Patrick Conway, Michael D. Tyka et al. Protein Science
  69. Atomic model of the type III secretion system needle (2012)
    Antoine Loquet, Nikolaos G. Sgourakis et al. Nature
  70. Intratumoral activation of the necroptotic pathway components RIPK1 and RIPK3 potentiates antitumor immunity (2019)
    Annelise G. Snyder, Nicholas Hubbard et al. Science Immunology
  71. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping (2010)
    Michael D. Tyka, D.A. Keedy et al. Journal of Molecular Biology
  72. Crystal structure of a monomeric retroviral protease solved by protein folding game players (2011)
    Firas Khatib, Frank DiMaio et al. Nature Structural & Molecular Biology
  73. Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes (2018)
    Jonathan T. Sockolosky, Eleonora Trotta et al. Science
  74. De Novo Enzyme Design Using Rosetta3 (2011)
    Florian Richter, Andrew Leaver‐Fay et al. PLoS ONE
  75. Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling (2017)
    Claudia Y. Janda, Luke T. Dang et al. Nature
  76. Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase (2016)
    Richard Obexer, А. Т. Година et al. Nature Chemistry
  77. Properties of a synthetic antigen related to the human blood-group Lewis a (1975)
    René Lemieux, David R. Bundle et al. Journal of the American Chemical Society
  78. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement (2015)
    Frank DiMaio, Yifan Song et al. Nature Methods
  79. Engineering an allosteric transcription factor to respond to new ligands (2015)
    Noah D. Taylor, Alexander S. Garruss et al. Nature Methods
  80. De novo design of a fluorescence-activating β-barrel (2018)
    Jiayi Dou, Anastassia A. Vorobieva et al. Nature
  81. Hallucinating symmetric protein assemblies (2022)
    Basile I. M. Wicky, Lukas F. Milles et al. Science

Immediate Impact

29 by Nobel laureates 51 from Science/Nature 89 standout
Sub-graph 1 of 20

Citing Papers

Evolutionary-scale prediction of atomic-level protein structure with a language model
2023 StandoutScience
Computational approaches streamlining drug discovery
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44 intermediate papers

Works of David Baker being referenced

Quantitative reactivity profiling predicts functional cysteines in proteomes
2010 StandoutNature
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
2006 Standout
and 72 more

Author Peers

Author Last Decade Papers Cites
David Baker 66365 22265 6344 771 83.6k
Janet M. Thornton 69527 20209 4198 480 90.5k
Klaus Schulten 62362 22827 2725 510 115.8k
Andrej Săli 49661 11352 2739 375 64.9k
J. Andrew McCammon 50018 13489 2657 834 70.4k
Kurt Wüthrich 64685 16157 4840 649 82.4k
G. Marius Clore 47355 14610 3465 547 60.2k
Christopher M. Dobson 64994 20067 3218 834 93.7k
Paul D. Adams 61519 17710 2893 353 84.9k
David A. Case 51383 14604 2669 332 79.2k
Martin Karplus 68659 27810 3073 780 106.4k

All Works

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