David Baker

143.1k total citations · 84 hit papers
791 papers, 86.6k citations indexed

About

David Baker is a scholar working on Molecular Biology, Materials Chemistry and Radiology, Nuclear Medicine and Imaging. According to data from OpenAlex, David Baker has authored 791 papers receiving a total of 86.6k indexed citations (citations by other indexed papers that have themselves been cited), including 594 papers in Molecular Biology, 272 papers in Materials Chemistry and 66 papers in Radiology, Nuclear Medicine and Imaging. Recurrent topics in David Baker's work include Protein Structure and Dynamics (350 papers), Enzyme Structure and Function (262 papers) and RNA and protein synthesis mechanisms (201 papers). David Baker is often cited by papers focused on Protein Structure and Dynamics (350 papers), Enzyme Structure and Function (262 papers) and RNA and protein synthesis mechanisms (201 papers). David Baker collaborates with scholars based in United States, United Kingdom and Canada. David Baker's co-authors include David E. Kim, Kim T. Simons, Tanja Kortemme, Brian Kuhlman, Frank DiMaio, Dylan Chivian, Rhiju Das, Carol A. Rohl, Sergey Ovchinnikov and Kira M.S. Misura and has published in prestigious journals such as Nature, Science and Cell.

In The Last Decade

David Baker

768 papers receiving 85.1k citations

Hit Papers

Protein structure prediction and ana... 1975 2026 1992 2009 2004 2010 1998 2004 2003 500 1000 1.5k
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. Protein structure prediction and analysis using the Robetta server
    2004 1.6k citations David E. Kim, David Baker et al. profile →
  2. Quantitative reactivity profiling predicts functional cysteines in proteomes
    2010 1.3k citations David Baker et al. Nature profile →
  3. Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright
    1998 1.3k citations David Baker et al. profile →
  4. Protein Structure Prediction Using Rosetta
    2004 1.3k citations David Baker et al. profile →
  5. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
    2003 1.3k citations Brian Kuhlman, Gabriele Varani et al. Science profile →
  6. Protein Structure Prediction and Structural Genomics
    2001 1.2k citations David Baker et al. Science profile →
  7. Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
    2009 1.1k citations David Baker et al. Proteins Structure Function and Bioinformatics profile →
  8. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions
    1997 1.1k citations David Baker et al. profile →
  9. The coming of age of de novo protein design
    2016 1.0k citations David Baker et al. Nature profile →
  10. Kemp elimination catalysts by computational enzyme design
    2008 975 citations Jasmine L. Gallaher, Alexandre Zanghellini et al. Nature profile →
  11. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
    2017 942 citations Frank DiMaio, Vikram Khipple Mulligan et al. profile →
  12. Improved protein structure prediction using predicted interresidue orientations
    2020 925 citations Ivan Anishchenko, Sergey Ovchinnikov et al. Proceedings of the National Academy of Sciences profile →
  13. De Novo Computational Design of Retro-Aldol Enzymes
    2008 890 citations Alexandre Zanghellini, Jasmine L. Gallaher et al. Science profile →
  14. Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
    2003 881 citations Brian Kuhlman, David Baker et al. profile →
  15. Predicting protein structures with a multiplayer online game
    2010 869 citations David Baker et al. Nature profile →
  16. High-Resolution Comparative Modeling with RosettaCM
    2013 813 citations Frank DiMaio, David E. Kim et al. profile →
  17. Macromolecular Modeling with Rosetta
    2008 748 citations David Baker et al. profile →
  18. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
    2010 692 citations Justin B. Siegel, Alexandre Zanghellini et al. Science profile →
  19. Consistent blind protein structure generation from NMR chemical shift data
    2008 669 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  20. Native protein sequences are close to optimal for their structures
    2000 657 citations Brian Kuhlman, David Baker Proceedings of the National Academy of Sciences profile →
  21. A simple physical model for binding energy hot spots in protein–protein complexes
    2002 653 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  22. Toward High-Resolution de Novo Structure Prediction for Small Proteins
    2005 636 citations David Baker et al. Science profile →
  23. A surprising simplicity to protein folding
    2000 592 citations David Baker Nature profile →
  24. An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae
    2012 548 citations Adam J. Wargacki, Effendi Leonard et al. Science profile →
  25. Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors
    2013 529 citations David Baker et al. Science profile →
  26. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
    2012 522 citations Neil P. King, David Baker et al. Science profile →
  27. High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis
    2014 504 citations David Baker et al. profile →
  28. Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
    2013 490 citations Hetunandan Kamisetty, Sergey Ovchinnikov et al. Proceedings of the National Academy of Sciences profile →
  29. Role of conformational sampling in computing mutation‐induced changes in protein structure and stability
    2010 476 citations David Baker et al. Proteins Structure Function and Bioinformatics profile →
  30. Computational Alanine Scanning of Protein-Protein Interfaces
    2004 460 citations David E. Kim, David Baker et al. profile →
  31. RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
    2011 454 citations Nobuyasu Koga, David Baker et al. profile →
  32. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
    2014 452 citations Sergey Ovchinnikov, Hetunandan Kamisetty et al. profile →
  33. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
    2020 451 citations Inna Goreshnik, Brian Coventry et al. Science profile →
  34. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
    2011 451 citations David Baker et al. Science profile →
  35. Accurate design of co-assembling multi-component protein nanomaterials
    2014 448 citations Neil P. King, David Baker et al. Nature profile →
  36. Plasma β-amyloid in Alzheimer’s disease and vascular disease
    2016 447 citations David Baker et al. profile →
  37. The trRosetta server for fast and accurate protein structure prediction
    2021 434 citations Ivan Anishchenko, David Baker et al. profile →
  38. Ab initio protein structure prediction of CASP III targets using ROSETTA
    1999 421 citations David Baker et al. Proteins Structure Function and Bioinformatics profile →
  39. An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
    2003 417 citations David Baker et al. profile →
  40. Accurate design of megadalton-scale two-component icosahedral protein complexes
    2016 415 citations Neil P. King, David Baker et al. Science profile →
  41. Principles for designing ideal protein structures
    2012 410 citations Nobuyasu Koga, David Baker et al. Nature profile →
  42. Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs
    2006 405 citations David Baker et al. profile →
  43. Computational Enzyme Design
    2013 401 citations Gert Kiss, David Baker et al. profile →
  44. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
    2011 389 citations David Baker et al. Nature profile →
  45. High-resolution mapping of protein sequence-function relationships
    2010 384 citations David Baker et al. profile →
  46. Mechanisms of protein folding
    2001 383 citations David Baker et al. profile →
  47. Structure prediction for CASP8 with all‐atom refinement using Rosetta
    2009 380 citations David E. Kim, Frank DiMaio et al. Proteins Structure Function and Bioinformatics profile →
  48. Plasma tau in Alzheimer disease
    2016 378 citations David Baker et al. profile →
  49. Algorithm discovery by protein folding game players
    2011 370 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  50. ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
    2006 367 citations David Baker et al. Proteins Structure Function and Bioinformatics profile →
  51. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    1999 358 citations David Baker et al. Proteins Structure Function and Bioinformatics profile →
  52. Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
    2016 352 citations Vikram Khipple Mulligan, David E. Kim et al. profile →
  53. Protein structure determination using metagenome sequence data
    2017 350 citations Sergey Ovchinnikov, David E. Kim et al. Science profile →
  54. Protein–Protein Docking with Backbone Flexibility
    2007 344 citations David Baker et al. profile →
  55. Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila
    1991 342 citations David Baker et al. profile →
  56. Automated de novo prediction of native-like RNA tertiary structures
    2007 341 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  57. The 3D profile method for identifying fibril-forming segments of proteins
    2006 340 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  58. Experiment and theory highlight role of native state topology in SH3 folding.
    1999 337 citations David Baker et al. profile →
  59. RosettaLigand Docking with Full Ligand and Receptor Flexibility
    2008 335 citations David Baker et al. profile →
  60. De novo protein design by deep network hallucination
    2021 334 citations Ivan Anishchenko, Sergey Ovchinnikov et al. Nature profile →
  61. Computational design of ligand-binding proteins with high affinity and selectivity
    2013 325 citations David Baker et al. Nature profile →
  62. Design of a hyperstable 60-subunit protein icosahedron
    2016 322 citations Yang Hsia, Rashmi Ravichandran et al. Nature profile →
  63. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    1999 318 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  64. Computational protein design enables a novel one-carbon assimilation pathway
    2015 315 citations Justin B. Siegel, Adam J. Wargacki et al. Proceedings of the National Academy of Sciences profile →
  65. Global analysis of protein folding using massively parallel design, synthesis, and testing
    2017 305 citations Inna Goreshnik, Lauren Carter et al. Science profile →
  66. Crystal structure of a monomeric retroviral protease solved by protein folding game players
    2011 301 citations Frank DiMaio, David Baker et al. Nature Structural & Molecular Biology profile →
  67. Intratumoral activation of the necroptotic pathway components RIPK1 and RIPK3 potentiates antitumor immunity
    2019 292 citations David Baker et al. profile →
  68. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
    2012 291 citations Hetunandan Kamisetty, David Baker et al. Nature Biotechnology profile →
  69. Reconstitution of SEC gene product-dependent intercompartmental protein transport
    1988 291 citations David Baker et al. profile →
  70. Relaxation of backbone bond geometry improves protein energy landscape modeling
    2013 288 citations Frank DiMaio, David Baker et al. profile →
  71. Atomic model of the type III secretion system needle
    2012 281 citations David Baker et al. Nature profile →
  72. Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes
    2018 275 citations Jonathan T. Sockolosky, Eleonora Trotta et al. Science profile →
  73. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
    2010 275 citations Frank DiMaio, David Baker et al. profile →
  74. Atomic accuracy in predicting and designing noncanonical RNA structure
    2010 273 citations David Baker et al. profile →
  75. De Novo Enzyme Design Using Rosetta3
    2011 263 citations David Baker et al. profile →
  76. Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling
    2017 263 citations Claudia Y. Janda, Luke T. Dang et al. Nature profile →
  77. RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
    2011 257 citations David Baker et al. profile →
  78. Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase
    2016 253 citations David Baker, Donald Hilvert et al. Nature Chemistry profile →
  79. Engineering an allosteric transcription factor to respond to new ligands
    2015 253 citations David Baker et al. profile →
  80. De novo design of a fluorescence-activating β-barrel
    2018 249 citations Matthew J. Bick, Lauren Carter et al. Nature profile →
  81. Properties of a synthetic antigen related to the human blood-group Lewis a
    1975 246 citations David Baker et al. profile →
  82. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement
    2015 244 citations Frank DiMaio, David Baker et al. profile →
  83. Elicitation of structure-specific antibodies by epitope scaffolds
    2010 225 citations David Baker et al. Proceedings of the National Academy of Sciences profile →
  84. Hallucinating symmetric protein assemblies
    2022 113 citations Justas Dauparas, Minkyung Baek et al. Science profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name h Career Trend Papers Cites
David Baker United States 157 67.9k 22.7k 6.5k 5.6k 5.4k 791 86.6k
Janet M. Thornton United Kingdom 117 70.9k 1.0× 20.5k 0.9× 4.3k 0.7× 4.5k 0.8× 7.1k 1.3× 488 92.5k
Klaus Schulten United States 126 63.9k 0.9× 23.6k 1.0× 2.8k 0.4× 8.0k 1.4× 5.0k 0.9× 532 120.6k
Andrej Săli United States 107 50.4k 0.7× 11.4k 0.5× 2.8k 0.4× 3.4k 0.6× 4.8k 0.9× 381 66.1k
J. Andrew McCammon United States 118 50.8k 0.7× 13.7k 0.6× 2.7k 0.4× 6.4k 1.1× 9.7k 1.8× 841 71.8k
Paul D. Adams United States 78 62.3k 0.9× 17.9k 0.8× 2.9k 0.5× 2.1k 0.4× 1.7k 0.3× 360 86.3k
David A. Case United States 96 52.2k 0.8× 14.9k 0.7× 2.7k 0.4× 8.4k 1.5× 9.8k 1.8× 340 81.1k
Randy J. Read United Kingdom 69 62.2k 0.9× 19.0k 0.8× 3.3k 0.5× 1.9k 0.3× 1.8k 0.3× 197 86.9k
Christopher M. Dobson United Kingdom 143 65.7k 1.0× 20.3k 0.9× 3.3k 0.5× 9.6k 1.7× 4.9k 0.9× 839 95.2k
Erik Lindahl Sweden 54 40.9k 0.6× 12.0k 0.5× 1.9k 0.3× 4.7k 0.8× 5.0k 0.9× 197 71.6k
Jane S. Richardson United States 57 43.5k 0.6× 12.8k 0.6× 2.4k 0.4× 2.2k 0.4× 2.1k 0.4× 130 59.8k

Countries citing papers authored by David Baker

Since Specialization
Citations

This map shows the geographic impact of David Baker's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by David Baker with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites David Baker more than expected).

Fields of papers citing papers by David Baker

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by David Baker. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by David Baker. The network helps show where David Baker may publish in the future.

Co-authorship network of co-authors of David Baker

This figure shows the co-authorship network connecting the top 25 collaborators of David Baker. A scholar is included among the top collaborators of David Baker based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with David Baker. David Baker is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Zhang, Jason Z., Josh T. Cuperus, Buwei Huang, et al.. (2025). De novo designed Hsp70 activator dissolves intracellular condensates. Cell chemical biology. 32(3). 463–473.e6. 3 indexed citations
2.
Kshirsagar, Meghana, Artur Meller, Ian R. Humphreys, et al.. (2025). Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm. Nature Communications. 16(1). 2017–2017. 1 indexed citations
3.
Dowling, Quinton M., Young‐Jun Park, Chelsea N. Fries, et al.. (2024). Hierarchical design of pseudosymmetric protein nanocages. Nature. 638(8050). 553–561. 17 indexed citations
4.
Goverde, Casper A., Martin Pačesa, L Dornfeld, et al.. (2024). Computational design of soluble and functional membrane protein analogues. Nature. 631(8020). 449–458. 40 indexed citations breakdown →
5.
Lin, Dingchang, Xiuyuan Li, Eric M. Moult, et al.. (2023). Time-tagged ticker tapes for intracellular recordings. Nature Biotechnology. 41(5). 631–639. 21 indexed citations
6.
Levy, Shiri, Ashish Phal, Sven Schmidt, et al.. (2022). dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region. Cell Reports. 38(9). 110457–110457. 14 indexed citations
7.
Stone, Elizabeth A., Parisa Hosseinzadeh, Timothy W. Craven, et al.. (2021). Isolating Conformers to Assess Dynamics of Peptidic Catalysts Using Computationally Designed Macrocyclic Peptides. ACS Catalysis. 11(8). 4395–4400. 20 indexed citations
8.
Balana, Aaron T., Paul M. Levine, Timothy W. Craven, et al.. (2021). O-GlcNAc modification of small heat shock proteins enhances their anti-amyloid chaperone activity. Nature Chemistry. 13(5). 441–450. 68 indexed citations
9.
Woodall, Nicholas B., Zara Y. Weinberg, Florian Büsch, et al.. (2021). De novo design of tyrosine and serine kinase-driven protein switches. Nature Structural & Molecular Biology. 28(9). 762–770. 18 indexed citations
10.
Basanta, Benjamin, Matthew J. Bick, Asim K. Bera, et al.. (2020). An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proceedings of the National Academy of Sciences. 117(36). 22135–22145. 53 indexed citations
11.
Maguire, Jack B., Hugh K. Haddox, Devin Strickland, et al.. (2020). Perturbing the energy landscape for improved packing during computational protein design. Proteins Structure Function and Bioinformatics. 89(4). 436–449. 87 indexed citations
12.
Cong, Qian, Ivan Anishchenko, Sergey Ovchinnikov, & David Baker. (2019). Protein interaction networks revealed by proteome coevolution. Science. 365(6449). 185–189. 150 indexed citations breakdown →
13.
Sockolosky, Jonathan T., Eleonora Trotta, Giulia Parisi, et al.. (2018). Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes. Science. 359(6379). 1037–1042. 275 indexed citations breakdown →
14.
Hosseinzadeh, Parisa, Gaurav Bhardwaj, Vikram Khipple Mulligan, et al.. (2017). Comprehensive computational design of ordered peptide macrocycles. Science. 358(6369). 1461–1466. 156 indexed citations
15.
Janda, Claudia Y., Luke T. Dang, Changjiang You, et al.. (2017). Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. Nature. 545(7653). 234–237. 263 indexed citations breakdown →
16.
Swaminathan, Vinay, Joseph Mathew Kalappurakkal, Shalin B. Mehta, et al.. (2017). Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions. Proceedings of the National Academy of Sciences. 114(40). 10648–10653. 92 indexed citations
17.
Anishchenko, Ivan, Sergey Ovchinnikov, Hetunandan Kamisetty, & David Baker. (2017). Origins of coevolution between residues distant in protein 3D structures. Proceedings of the National Academy of Sciences. 114(34). 9122–9127. 132 indexed citations
18.
Martinello, Marianne, Gregory J. Dore, Rohan I. Bopage, et al.. (2016). Antiretroviral Use in the CEASE Cohort Study and Implications for Direct-Acting Antiviral Therapy in Human Immunodeficiency Virus/Hepatitis C Virus Coinfection. Open Forum Infectious Diseases. 3(2). ofw105–ofw105. 13 indexed citations
19.
Wargacki, Adam J., Effendi Leonard, Maung Nyan Win, et al.. (2012). An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae. Science. 335(6066). 308–313. 548 indexed citations breakdown →
20.
Siegel, Justin B., Alexandre Zanghellini, Helena M. Lovick, et al.. (2010). Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction. Science. 329(5989). 309–313. 692 indexed citations breakdown →

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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Breakdown of academic impact, for papers by Janet M. Thornton Breakdown of academic impact, for papers by Klaus Schulten Breakdown of academic impact, for papers by Andrej Săli Breakdown of academic impact, for papers by J. Andrew McCammon Breakdown of academic impact, for papers by Paul D. Adams Breakdown of academic impact, for papers by David A. Case Breakdown of academic impact, for papers by Randy J. Read Breakdown of academic impact, for papers by Christopher M. Dobson Breakdown of academic impact, for papers by Erik Lindahl Breakdown of academic impact, for papers by Jane S. Richardson
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