Revised 1/27/2015
David Baker, Ph.D.
Department of Biochemistry
Box 351655
University of Washington
Seattle, WA 98195
Phone: 206-543-1295
E-mail address: dabaker@uw.edu
Education
1984
1989
B.A.
Ph.D.
Harvard University
University of California, Berkeley
Postgraduate Training
1990-1993
Postdoctoral work in the Department of Biochemistry and Biophysics, University of
California, San Francisco, laboratory of Dr. David Agard.
Faculty Positions
1993-2000
2000-2003
2000-2005
200320032005-
Assistant Professor, Department of Biochemistry, University of Washington.
Associate Professor, Department of Biochemistry, University of Washington
Associate Investigator, Howard Hughes Medical Institute
Professor, Department of Biochemistry, University of Washington
Adjunct Professor of Bioengineering, Genome Sciences, Chemical Engineering and
Physics
Investigator, Howard Hughes Medical Institute
Awards, Honors and Professional Activities
1983, 1984
1985
1985-1988
1990-1993
1993
1994199419951999200020002000
2002
20032004
2004
2006
2007
2008
2009
Harvard College Scholarship
University of California Regents fellowship
National Science Foundation pre-doctoral fellowship
Life Sciences Research Foundation postdoctoral fellowship
Boyer Foundation fellowship
National Science Foundation Young Investigator Award
Packard Fellowship in Science and Engineering
Beckman Young Investigator Award
Nominating Committee, Protein Society
Editorial Advisory Board, Protein Science
HHMI Assistant Investigator
Protein Society Young Investigator Award
International Society for Computational Biology Overton Prize
Director, Biomolecular structure and design graduate program (BMSD)
AAAS Newcomb-Cleveland prize
Foresight Institute Feynman Prize
National Academy of Sciences
Editorial Board, PNAS
Sackler Prize in Biophysics
American Academy of Sciences
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2011
2012
2014
University of Washington Inventor of the Year Award
Biochemical Society Centenary Award
American Chemical Society David Perlman Memorial Award
Teaching Responsibilities
BIOC 499 Undergraduate Research
BIOC 530 Introduction to Structural Biology
Faculty Positions of Former Students and Postdocs
Eric Alm, Ph.D – Associate Professor, MIT
Ingemar Andre, Ph.D. – Assistant Professor, Lund University
Patrick Barth, Ph.D. – Assistant Professor, Baylor College of Medicine
Richard Bonneau, Ph.D. – Associate Professor, NYU
Phil Bradley, Ph.D. – Assistant Professor, Fred Hutchinson Cancer Research Center
Christopher Bystroff, Ph.D. – Associate Professor, Rensselaer Polytechnical Institute
Gautam Dantas, Ph.D. – Assistant Professor, Washington University
Rhiju Das, Ph.D. – Assistant Professor, Stanford University
Frank Dimaio, Ph.D. – Assistant Professor, University of Washington
Sarel Fleishman, Ph.D. – Assistant Professor, Weizmann Institute
Jeff Gray, Ph.D. – Associate Professor, Johns Hopkins
Dominik Gront, Ph.D. – Assistant Professor, University of Warsaw
Jim Havranek, Ph.D. – Assistant Professor, Washington University
John Karanicolas, Ph.D. – Assistant Professor, University of Kansas
Sagar Khare, Ph.D. – Assistant Professor, Rutgers
Firas Khatib, Ph.D. – Assistant Professor, University of Massachusetts at Dartmouth
Tanja Kortemme, Ph.D. – Professor, University of California, San Francisco
Takahiro Kosugi, Ph.D. – Assistant Professor, National Institutes of Natural Sciences, Japan
Brian Kuhlman, Ph.D. – Professor, University of North Carolina, Chapel Hill
Oliver Lange, Ph.D. – Assistant Professor, TU Munich, Germany
Jens Meiler, Ph.D. – Associate Professor, Vanderbilt University
Jeremy Mills, Ph.D. – Assistant Professor, Arizona State University
Alex Morozov, Ph.D. – Associate Professor, Rutgers University
Kevin Plaxco, Ph.D. – Professor, University of California, Santa Barbara
Erik Procko, Ph.D. – Assistant Professor, University of Illinois Urbana-Champaign
Ingo Ruczinski, Ph.D. – Associate Professor, Johns Hopkins
Bill Schief, Ph.D. – Associate Professor, Scripps Research Institute
Max Schlosshauer, Ph.D. – Assistant Professor, University of Portland
Ora Schueler-Furman, Ph.D. – Assistant Professor, Hebrew University
Justin Siegel, Ph.D. – Assistant Professor, University of California, Davis
Kim Simons, Ph.D. – Assistant Professor, Emporia State University
Adrien Treuille, Ph.D. – Assistant Professor, Carnegie Mellon University
Jerry Tsai, Ph.D. – Associate Professor, University of the Pacific
Bjorn Wallner, Ph.D. – Associate Professor, Linkoping University
Chu Wang, Ph.D. – Assitant Professor, Peking University
William Wedemeyer, Ph.D.- Assistant Professor, Michigan State University
Tim Whitehead, Ph.D. – Assistant Professor, Michigan State University
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Vladimir Yarov-Yarovoy, Ph.D. – Assistant Professor, University of California, Davis
Funding
NIH 5 P41 GM103533-18 (Davis, PI), Comprehensive Biology: Exploiting the Yeast Genome, 09/01/200606/30/2016, $83,916 Baker Annual Direct Costs, 8% effort.
NIH R01 AI096184-01 (Yager, PI), A 2DPN-Based High Sensitivity Low-Cost Multiplexed POC Immunoassay
Platform, 07/15/2011-06/30/2016, $82,723 Annual Direct Costs, 2% effort.
AFOSR FA950-12-10112 (S. Banta, PI), 3-d-Enzymatic Nanomaterial Architectures for Energy Harvesting, 4/1/123/31/16, $147,699 Annual Direct Costs, 5% effort.
NSF CHE-1332907 (Baker, PI) Integrating Theory, Computation and Experiment to Robustly Design Complex
Protein-based Nanomaterials, 10/01/13 – 09/30/16, $363,460 Annual Direct Costs, 5% effort
HDTRA1-11-C-0026 AM05 (Sussman, PI) Engineering of Highly Proficient Catalytic Bioscavengers for In Vivo
Detoxification of a Broad Spectrum of Nerve Agents, 06/01/11 – 08/06/16, $201,607 Annual Direct Costs, 2%
effort
LSDF 9598385 (Baker, PI) Launch of the Institute for Protein Design, 04/01/14 – 3/31/19, $559,209 Annual Direct
Costs, 10% effort
Bill & Melinda Gates Foundation OPP1118840 (Baker, PI) Testing the Nearest Neighbor Approach to Active
Vaccination for HIV-1 bNAbs, 11/7/14-09/30/17, $347,533 Annual Direct Costs, 2% effort
Bill & Melinda Gates Foundation OPP1111923 (Baker, PI) Next Generation CD8 Directed Nanoparticle Vaccines
for HIV, 11/7/14-09/30/18, $431,695 Annual Direct Costs, 2% effort
Bill & Melinda Gates Foundation OPP1120319 (Baker, PI) Development of a Nanoparticle RSV-MPV F Protein
Vaccine Candidate, 11/18/14-10/31/17, $414,337 Annual Direct Costs, 2% effort
HDTRA1-11-1-0041 (Baker, PI) Towards a Next Generation of Potent Computationally Designed Enzyme
Catalysts, 08/22/11 – 08/21/16, $136,064 Annual Direct Costs, 5% effort
NIH/NIGMS 1R01GM092802 (Baker, PI) High resolution structure modeling with Rosetta, 06/01/14 – 03/31/19,
$185,560 Annual Direct Costs, 15% effort
NSF MCB-1445201 (Jerala, PI) BioMolecular Origami, 07/15/14 – 06/30/17, $81,231 Annual Direct Costs, 2%
effort
NSF CHE-1523362 (Baker, PI) Foldit Game Empowering the Citizen Scientist in the Fight Against Ebolaviruses,
4/1/15-3/31/16, $132,691 Total Direct Costs, 2% effort
DARPA W911NF-15-1-0645 (King, PI) Computationally Designed Protein Nanoparticles for Biological
Macromolecule Delivery, 11/1/15 – 7/31/16, $194,175 Total Direct Costs, 1% effort
Peer-Reviewed Publications
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Baker D, Hicke L, Rexach M, Schleyer M, Schekman R. 1988. Reconstitution of SEC Gene ProductDependent Intercompartmental Protein-Transport. Cell 54(3):335-344.
Payne GS, Baker D, Van Tuinen E, Schekman R. 1988. Protein Transport to the Vacuole and ReceptorMediated Endocytosis by Clathrin Heavy Chain-Deficient Yeast. Journal of Cell Biology 106(5):14531462.
Baker D, Wuestehube L, Schekman R, Botstein D, Segev N. 1990. GTP-binding Ypt1 Protein and Ca2+
Function Independently in a Cell-free Protein Transport Reaction. Proc Natl Acad Sci U S A 87(1):355359.
Ruohola H, Bremer KA, Baker D, Swedlow JR, Jan LY, Jan YN. 1991. Role of Neurogenic Genes in
Establishment of Follicle Cell Fate and Oocyte Polarity During Oogenesis in Drosophila. Cell 66(3):433450.
Baker D, Silen JL, Agard DA. 1992. Protease Pro-Region Required for Folding is a Potent Inhibitor of the
Mature Enzyme. Proteins-Structure Function and Genetics 12(4):339-344.
Baker D, Sohl JL, Agard DA. 1992. A Protein-Folding Reaction Under Kinetic Control. Nature (London)
356(6366):263-265.
Baker D, Bystroff C, Fletterick RJ, Agard DA. 1993. PRISM: Topologically Constrained Phase Refinement
for Macromolecular Crystallography. Acta Crystallographica Section D Biological Crystallography
49(5):429-439.
Baker D, Chan HS, Dill KA. 1993. Coordinate-Space Formulation of Polymer Lattice Cluster Theory.
Journal of Chemical Physics 98(12):9951-9962.
Baker D, Krukowski AE, Agard DA. 1993. Uniqueness and the Ab initio Phase Problem in Macromolecular
Crystallography. Acta Crystallographica Section D Biological Crystallography 49(1):186-192.
Bystroff C, Baker D, Fletterick RJ, Agard DA. 1993. PRISM: Application to the Solution of Two Protein
Structures. Acta Crystallographica Section D Biological Crystallography 49(5):440-448.
Ruohola-Baker H, Greil E, Chou T-B, Baker D, Jan LY, Jan YN. 1993. Spatially Localized Rhomboid is
Required for Establishment of the Dorsal-ventral Axis in Drosophila Oogenesis. Cell 73(5):953-965.
Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, Baker D. 1995. A Phage Display System for Studying the
Sequence Determinants of Protein Folding. Protein Sci 4(6):1108-1117.
Han KF, Baker D. 1995. Recurring Local Sequence Motifs in Proteins. Journal of Molecular Biology
251(1):176-187.
Bystroff C, Simons KT, Han KF, Baker D. 1996. Local Sequence-Structure Correlations in Proteins. Current
Opinion in Biotechnology 7(4):417-421.
Han KF, Baker D. 1996. Global Properties of the Mapping Between Local Amino Acid Sequence and Local
Structure in Proteins. Proc Natl Acad Sci USA 93(12):5814-5818.
Yi Q, Baker D. 1996. Direct Evidence for a Two-State Protein Unfolding Transition from HydrogenDeuterium Exchange, Mass Spectrometry, and NMR. Protein Science 5(6):1060-1066.
Bystroff C, Baker D. 1997. Blind Predictions of Local Protein Structure in CASP2 Targets Using the I-Sites
Library. Proteins-Structure Function and Genetics:167-171.
Doyle, R., Simons, K., Qian, H., and Baker, D. 1997. Local interactions and the optimization of protein
folding. Proteins, 29:282-191.
Grantcharova VP, Baker D. 1997. Folding Dynamics of the src SH3 Domain. Biochemistry 36(50):1568515692.
Gu H, Kim D, Baker D. 1997. Contrasting Roles for Symmetrically Disposed beta-turns in the Folding of a
Small Protein. J Mol Biol 274(4):588-596.
Han KF, Bystroff C, Baker D. 1997. Three-dimensional Structures and Contexts Associated with Recurrent
Amino Acid Sequence Patterns. Protein Science 6(7):1587-1590.
Rank JA, Baker D. 1997. A Desolvation Barrier to Hydrophobic Cluster Formation May Contribute to the
Rate-Limiting Step in Protein Folding. Protein Science 6(2):347-354.
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Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D. 1997. Functional Rapidly
Folding Proteins From Simplified Amino Acid Sequences. Nat Struct Biol 4(10):805-809.
Scalley ML, Baker D. 1997. Protein Folding Kinetics Exhibit an Arrhenius Temperature Dependence When
Corrected for the Temperature Dependence of Protein Stability. Proc Natl Acad Sci USA 94(20):1063610640.
Scalley ML, Yi Q, Gu HD, McCormack A, Yates JR, Baker D. 1997. Kinetics of Folding of the IgG Binding
Domain of Peptostreptoccocal Protein L. Biochemistry 36(11):3373-3382.
Simons KT, Kooperberg C, Huang E, Baker D. 1997. Assembly of Protein Tertiary Structures From
Fragments With Similar Local Sequences Using Simulated Annealing and Bayesian Scoring Functions.
Journal of Molecular Biology 268(1):209-225.
Yi Q, Scalley ML, Simons KT, Gladwin ST, Baker D. 1997. Characterization of the Free Energy Spectrum of
Peptostreptococcal Protein L. Folding & Design 2(5):271-280.
Bystroff, C. and Baker, D. 1998. Local structure prediction using a library of sequence-structure motifs.
J. Mol. Biol. 281, 565-577.
Grantcharova VP, Riddle DS, Santiago JV, Baker D. 1998. Important Role of Hydrogen Bonds in the
Structurally Polarized Transition State for Folding of the src SH3 Domain. Nature Structural Biology
5(8):714-720.
Kim DE, Gu H, Baker D. 1998. The Sequences of Small Proteins are not Extensively Optimized for Rapid
Folding by Natural Selection. Proc Natl Acad Sci U S A 95(9):4982-4986.
Kim DE, Yi Q, Gladwin ST, Goldberg JM, Baker D. 1998. The Single Helix in Protein L is Largely Disrupted
at the Rate-Limiting Step in Folding. Journal of Molecular Biology 284(3):807-815.
Plaxco KW, Baker D. 1998. Limited Internal Friction in the Rate-Limiting Step of a Two-state Protein
Folding Reaction. Proc Natl Acad Sci USA 95(23):13591-13596.
Plaxco KW, Simons KT, Baker D. 1998. Contact Order, Transition State Placement and the Refolding
Rates of Single Domain Proteins. Journal of Molecular Biology 277(4):985-994.
Rank JA, Baker D. 1998. Contributions of Solvent-Solvent Hydrogen Bonding and van der Waals
Interactions to the Attraction Between Methane Molecules in Water. Biophysical Chemistry 71(2-3):199204.
Shortle D, Simons KT, Baker D. 1998. Clustering of Low-Energy Conformations Near the Native Structures
of Small Proteins. Proc Natl Acad Sci USA 95(19):11158-11162.
Simons, K.T., Ruczinski, I. Kooperberg, C., Fox, B., Bystroff, C. and Baker, D. 1998. Improved recognition
of native-like protein structures using a combination of sequence-dependent and sequenceindependent features of proteins. Proteins 34:82-95.
Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. 1998. Prediction and Structural Characterization of an
Independently Folding Substructure in the src SH3 Domain. Journal of Molecular Biology 283(1):293-300.
Alm E, Baker D. 1999. Prediction of Protein-Folding Mechanisms from Free-Energy Landscapes Derived
From Native Structures. Proc Natl Acad Sci. USA 96(20):11305-11310.
Gu H, Doshi N, Kim DE, Simons KT, Santiago JV, Nauli S, Baker D. 1999. Robustness of Protein Folding
Kinetics to Surface Hydrophobic Substitutions. Protein Science 8(12):2734-2741.
Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D. 1999. Chain Collapse can Occur Concomitantly with
the Rate-Limiting Step in Protein Folding. Nature Structural Biology 6(6):554-556.
Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. 1999. Experiment and Theory
Highlight Role of Native State Topology in SH3 Folding. Nature Structural Biology 6(11):1016-1024.
Scalley ML, Nauli S, Gladwin ST, Baker D. 1999. Structural Transitions in the Protein L Denatured State
Ensemble. Biochemistry 38(48):15927-15935.
Simons KT, Bonneau R, Ruczinski I, Baker D. 1999. Ab initio Protein Structure Prediction of CASP III
Targets using ROSETTA. Proteins 0(SUPPL. 3):171-176.
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Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. 1999. Improved Recognition of Nativelike Protein Structures Using a Combination of Sequence-Dependent and Sequence-Independent
Features of Proteins. Proteins 34(1):82-95.
Tsai J, Levitt M, Baker D. 1999. Hierarchy of Structure Loss in MD Simulations of src SH3 Domain
Unfolding. Journal of Molecular Biology 291(1):215-225.
Bowers PM, Strauss CE, Baker D. 2000. De novo Protein Structure Determination Using Sparse NMR
data. J Biomol NMR 18(4):311-318.
Bystroff C, Thorsson V, Baker D. 2000. HMMSTR: A Hidden Markov Model for Local Sequence-Structure
Correlations in Proteins. Journal of Molecular Biology 301(1):173-190.
Grantcharova VP, Riddle DS, Baker D. 2000. Long-range Order in the src SH3 Folding Transition State.
Proc Natl Acad Sci USA 97(13):7084-7089.
Johnsen K, O'Neill JW, Kim DE, Baker D, Zhang KY. 2000. Crystallization and Preliminary X-ray Diffraction
Studies of Mutants of B1 IgG-binding Domain of Protein L From Peptostreptococcus Magnus. Acta
Crystallogr D Biol Crystallogr 56(Pt 4):506-508.
Kim DE, Fisher C, Baker D. 2000. A Breakdown of Symmetry in the Folding Transition State of Protein L.
Journal of Molecular Biology 298(5):971-984.
Kuhlman B, Baker D. 2000. Native Protein Sequences are Close to Optimal for their Structures. Proc Natl
Acad Sci USA 97(19):10383-10388.
McCallister EL, Alm E, Baker D. 2000. Critical Role of Beta-hairpin Formation in Protein G Folding. Nature
Structural Biology 7(8):669-673.
Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D. 2000.
Evolutionary Conservation in Protein Folding Kinetics. Journal of Molecular Biology 298(2):303-312.
Plaxco KW, Simons KT, Ruczinski I, Baker D. 2000. Topology, Stability, Sequence, and Length: Defining
the Determinants of Two-state Protein Folding Kinetics. Biochemistry 39(37):11177-11183.
Thayer EC, Bystroff C, Baker D. 2000. Detection of Protein Coding Sequences Using a Mixture Model for
Local Protein Amino Acid Sequence. Journal of Computational Biology 7(1-2):317-327.
Yi Q, Scalley-Kim ML, Alm EJ, Baker D. 2000. NMR Characterization of Residual Structure in the
Denatured State of Protein L. Journal of Molecular Biology 299(5):1341-1351.
Bonneau R, Strauss CEM, Baker D. 2001. Improving the Performance of Rosetta Using Multiple Sequence
Alignment Information and Global Measures of Hydrophobic Core Formation. Proteins-Structure
Function and Genetics 43(1):1-11.
Bonneau R, Tsai J, Ruczinski I, Baker D. 2001. Functional Inferences From Blind ab initio Protein Structure
Predictions. Journal of Structural Biology 134(2-3):186-190.
Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CEM, Baker D. 2001. Rosetta in CASP4: Progress
in ab initio Protein Structure Prediction. Proteins-Structure Function and Genetics:119-126.
Grantcharova VP, Baker D. 2001. Circularization Changes the Folding Transition State of the src SH3
Domain. Journal of Molecular Biology 306(3):555-563.
Kim KM, Yi EC, Baker D, Zhang KYJ. 2001. Post-translational Modification of the N-terminal His Tag
Interferes with the Crystallization of the Wild-type and Mutant SH3 Domains from Chicken src Tyrosine
Kinase. Acta Crystallographica Section D Biological Crystallography 57(5):759-762.
Kuhlman B, O'Neill JW, Kim DE, Zhang KYJ, Baker D. 2001. Conversion of Monomeric Protein L to an
Obligate Dimer by Computational Protein Design. Proc Natl Acad Sci USA 98(19):10687-10691.
Lee MR, Baker D, Kollman PA. 2001. 2.1 and 1.8 A Average C(alpha) RMSD Structure Predictions on Two
Small Proteins, HP-36 and s15. J Am Chem Soc 123(6):1040-1046.
Lee MR, Tsai J, Baker D, Kollman PA. 2001. Molecular Dynamics in the Endgame of Protein Structure
Prediction. Journal of Molecular Biology 313(2):417-430.
Minard P, Scalley-Kim M, Watters A, Baker D. 2001. A "Loop Entropy Reduction" Phage-display Selection
for Folded Amino Acid Sequences. Protein Science 10(1):129-134.
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Nauli S, Kuhlman B, Baker D. 2001. Computer-based Redesign of a Protein Folding Pathway. Nature
Structural Biology 8(7):602-605.
O'Neill, J. W., Kim, D.E., Baker, D. and Zhang, K.Y. (2001). Structures of the B1 domain of protein L from
Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Acta Crystallogr. D Biol.
Crystallogr. 57(Pt 4):480-487.
Simons KT, Strauss C, Baker D. 2001. Prospects for ab initio Protein Structural genomics. Journal of
Molecular Biology 306(5):1191-1199.
Alm E, Morozov AV, Kortemme T, Baker D. 2002. Simple Physical Models Connect Theory and
Experiment in Protein Folding Kinetics. Journal of Molecular Biology 322(2):463-476.
Bonneau R, Ruczinski I, Tsai J, Baker D. 2002. Contact Order and ab initio Protein Structure Prediction.
Protein Science 11(8):1937-1944.
Bonneau R, Strauss CEM, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. 2002. De
novo Prediction of Three-Dimensional Structures for Major Protein Families. Journal of Molecular
Biology 322(1):65-78.
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. 2002. Design, Activity, and
Structure of a Highly Specific Artificial Endonuclease. Molecular Cell 10(4):895-905.
Kortemme T, Baker D. 2002. A Simple Physical Model for Binding Energy Hot Spots in Protein-Protein
Complexes. Proc Natl Acad Sci USA 99(22):14116-14121.
Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR. 2002. Understanding Protein Hydrogen
Bond Formation with Kinetic H/D Amide Isotope Effects. Nature Structural Biology 9(6):458-463.
Kuhlman B, O'Neill JW, Kim DE, Zhang KYJ, Baker D. 2002. Accurate Computer-Based Design of a New
Backbone Conformation in the Second Turn of Protein L. Journal of Molecular Biology 315(3):471-477.
Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW. 2002. Residues Participating in the Protein
Folding Nucleus do not Exhibit Preferential Evolutionary Conservation. Journal of Molecular Biology
316(2):225-233.
Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D. 2002. Crystal Structures and Increased
Stabilization of the Protein G Variants with Switched Folding Pathways NuG1 and NuG2. Protein Science
11(12):2924-2931.
Rohl CA, Baker D. 2002. De novo Determination of Protein Backbone Structure From Residual Dipolar
Couplings Using Rosetta. Journal of the American Chemical Society 124(11):2723-2729.
Ruczinski I, Kooperberg C, Bonneau R, Baker D. 2002. Distributions of Beta Sheets in Proteins with
Application to Structure Prediction. Proteins 48(1):85-97.
Saunders CT, Baker D. 2002. Evaluation of Structural and Evolutionary Contributions to Deleterious
Mutation Prediction. Journal of Molecular Biology 322(4):891-901.
Schlosshauer M, Baker D. 2002. A General Expression for Bimolecular Association Rates with
Orientational Constraints. Journal of Physical Chemistry B 106(46):12079-12083.
Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, Garcia KC. 2003. Convergent Mechanisms for
Recognition of Divergent Cytokines by the Shared Signaling Receptor gp130. Molecular Cell 12(3):577589.
Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O,
Murphy P, Schonbrun J, Baker D. 2003. Rosetta Predictions in CASP5: Successes, Failures, and Prospects
for Complete Automation. Proteins 53 Suppl 6:457-468.
Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA,
Baker D. 2003. Automated Prediction of CASP-5 Structures Using the Robetta Server. Proteins 53 Suppl
6:524-533.
Dantas G, Kuhlman B, Callender D, Wong M, Baker D. 2003. A Large Scale Test of Computational Protein
Design: Folding and Stability of Nine Completely Redesigned Globular Proteins. Journal of Molecular
Biology 332(2):449-460.
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Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. 2003. Protein-Protein
Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations.
Journal of Molecular Biology 331(1):281-299.
Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KMS, Morozov AV, Baker D. 2003.
Protein-Protein Docking Predictions for the CAPRI Experiment. Proteins 52(1):118-122.
Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH,
Chiu CH, Baker D. 2003. Assigning Function to Yeast Proteins by Integration of Technologies. Mol Cell
12(6):1353-1365.
Ivankov, D. N., Garbuzynskiy, S.O., Alm, E., Plaxco, K.W., Baker, D. and Finkelstein, A.V. 2003. Contact
order revisited: influence of protein size on the folding rate. Protein Sci 12:2057-2062.
Kortemme T, Morozov AV, Baker D. 2003. An Orientation-Dependent Hydrogen Bonding Potential
Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes. Journal of
Molecular Biology 326(4):1239-1259.
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. 2003. Design of a Novel Globular
Protein Fold With Atomic-Level Accuracy. Science 302(5649):1364-1368.
McFarland BJ, Kortemme T, Yu SF, Baker D, Strong RK. 2003. Symmetry Recognizing Asymmetry: Analysis
of the Interactions Between the C-type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands.
Structure 11(4):411-422.
Meiler J, Baker D. 2003. Coupled Prediction of Protein Secondary and Tertiary Structure. Proc Natl Acad
Sci USA 100(21):12105-12110.
Meiler, J. and Baker, D. (2003). Rapid protein fold determination using unassigned NMR data. Proc. Natl.
Acad. Sci. USA 100:15404-15409.
Millet O, Mittermaier A, Baker D, Kay LE. 2003. The Effects of Mutations on Motions of Side-Chains in
Protein L Studied by 2H NMR Dynamics and Scalar Couplings. J Mol Biol 329(3):551-63.
Morozov AV, Kortemme T, Baker D. 2003. Evaluation of Models of Electrostatic Interactions in Proteins.
Journal of Physical Chemistry B 107(9):2075-2090.
Sadreyev RI, Baker D, Grishin NV. 2003. Profile-profile comparisons by COMPASS predict intricate
homologies between protein families. Protein Science 12(10):2262-2272.
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Generated Proteins Suggests High Folding Free Energy Barriers and Cooperativity may be Consequences
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Model Neglecting Long-Range Interactions, Free Energy Barriers, and Landscape Ruggedness. Protein
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Binding of Protein L to Ig Kappa Light Chain. Biochemistry 43(9):2445-2457.
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Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Jr., Stoddard BL, Baker D. 2006.
Computational Redesign of Endonuclease DNA Binding and Cleavage Specificity. Nature (London)
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NonLocal Strand Pairings and Local Backbone Conformation. Proteins-Structure Function and
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Stable Homodimer: Implications for Protein Engineering and Evolution. Journal of Molecular Biology
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Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP. 2006. Folding of the CTerminal Bacterial Binding Domain in Statherin Upon Adsorption Onto Hydroxyapatite Crystals. Proc Natl
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Cooperativity of alpha Helix Formation. Journal of Physical Chemistry B 110(10):4503-4505.
Palmer AE, Giacomello M, Kortemme T, Hires SA, Lev-Ram V, Baker D, Tsien RY. 2006. Ca2+ Indicators
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Sood VD, Baker D. 2006. Recapitulation and Design of Protein Binding Peptide Structures and
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Sprague ER, Wang C, Baker D, Bjorkman PJ. 2006. Crystal Structure of the HSV-1 Fc Receptor Bound to Fc
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Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. 2006. The 3D Profile Method
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Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D. 2006. New
Algorithms and an in silico Benchmark for Computational Enzyme Design. Protein Science 15(12):27852794.
Andre I, Bradley P, Wang C, Baker D. 2007. Prediction of the Structure of Symmetrical Protein
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Barth P, Schonbrun J, Baker D. 2007. Toward High-Resolution Prediction and Design of Transmembrane
Helical Protein Structures. Proc Natl Acad Sci USA 104(40):15682-15687.
Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker
D. 2007. High-Resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human
Procarboxypeptidase by Computational Protein Design. Journal of Molecular Biology 366(4):1209-1221.
Das R, Baker D. 2007. Automated de novo Prediction of Native-Like RNA Tertiary Structures. Proc Natl
Acad Sci USA 104(37):14664-14669.
Das R, Bin Q, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Baker D.
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Proteins-Structure Function and Bioinformatics 69:118-128.
Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM,
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to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity. J
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Malmstrom L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. 2007. Superfamily
Assignments for the Yeast Proteome Through Integration of Structure Prediction With the Gene
Ontology. Plos Biology 5(4):758-768.
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. 2007. High-Resolution Structure
Prediction and the Crystallographic Phase Problem. Nature 450(7167):259-264.
Shcherbata HR, Yatsenko AS, Patterson L, Sood VD, Nudel U, Yaffe D, Baker D, Ruohola-Baker H. 2007.
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Chembiochem 8(10):1162-1169.
Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D and others. 2007.
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Tsemekhman K, Goldschmidt L, Eisenberg D, Baker D. 2007. Cooperative Hydrogen Bonding in Amyloid
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Wang C, Bradley P, Baker D. 2007. Protein-Protein Docking with Backbone Flexibility. Journal of
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Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D. 2007. The Highly Cooperative
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Wojtowicz WM, Wu W, Andre I, Qian B, Baker D, Zipursky SL. 2007. A Vast Repertoire of Dscam Binding
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Wollacott AM, Zanghellini A, Murphy P, Baker D. 2007. Prediction of Structures of Multidomain Proteins
from Structures of the Individual Domains. Protein Science 16(2):165-175.
Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker
H. 2007. A Putative Src Homology 3 Domain Binding Motif but not the C-terminal Dystrophin WW
Domain Binding Motif is Required for Dystroglycan Function in Cellular Polarity in Drosophila. Journal of
Biological Chemistry 282(20):15159-15169.
Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB,
Herschlag D. 2008. Structural Inference of Native and Partially Folded RNA by High-Throughput Contact
Mapping. Proc Natl Acad Sci USA 105(11):4144-4149.
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. 2008. A
New Twist in TCR Diversity Revealed by a Forbidden alpha beta TCR. Journal of Molecular Biology
375(5):1306-1319.
Raman S, Qian B, Baker D, Walker RC. 2008. Advances in Rosetta Protein Structure Prediction on
Massively Parallel Systems. Ibm Journal of Research and Development 52(1-2):7-17.
Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL. 2008. Catalytic Mechanism and Performance
of Computationally Designed Enzymes for Kemp Elimination. Journal of American Chemical Society
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André I, Strauss CE, Kaplan DB, Bradley P, Baker D. 2008. Emergence of Symmetry in Homooligomeric
Biological Assemblies. Proc Natl Acad Sci USA.105(42):16148-16152.
Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. 2008. A Double
S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms. Cell
134(6):1007-1018.
Cho HD, Sood VD, Baker D, Weiner AM. 2008. On the Role of a Conserved, Potentially Helix-breaking
Residue in the tRNA-helix of Archaeal CCA-adding Enzymes. RNA 14(7):1284-1289.
Keeble AH, Joachimiak LA, Maté MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C. 2008.
Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity
Proteins by Colicin Endonucleases. Journal of Molecular Biology 379(4):745-759.
Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA,
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Protein Structure Generation From NMR Chemical Shift Data. Proc Natl Acad Sci USA. 105(12):46854690.
Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F,
Barbas CF 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D. 2008. De novo Computational Design of Retroaldol Enzymes. Science 319(5868):1387-1391.
Qiu J, Sheffler W, Baker D, Noble WS. 2008. Ranking Predicted Protein Structures with Support Vector
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Fan E, Baker D, Fields S, Gelb MH, Buckner FS, Van Voorhis WC, Phizicky E, Dumont M, Mehlin C,
Grayhack E, Sullivan M, Verlinde C, Detitta G, Meldrum DR, Merritt EA, Earnest T, Soltis M, Zucker F,
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WG. 2008. Structural Genomics of Pathogenic Protozoa: An Overview. Methods Mol Biol. 426: 497-513.
Davis IW, Baker D. 2009. Rosetta Ligand Docking With Full Ligand and Receptor Flexibility. Journal of
Molecular Biology 385(2):381-392.
Shen Y, Vernon R, Baker D, Bax A. 2009. De novo Protein Structure Generation from Incomplete
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Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA.
2009. Improving NMR Protein Structure Quality by Rosetta Refinement: A Molecular Replacement
Study. Proteins 75(1):147-167.
Barth P, Wallner B, Baker, D. 2009. Prediction of membrane protein structures with complex topologies
using limited constraints. Proc. Natl. Acad. Sci. USA 106(5):1409-1414.
Sheffler W, Baker D. 2009. Rosetta Holes: Rapid assessment of protein core packing for structure
prediction, refinement, design, and validation. Protein Science 18(1):229-239.
Spreter T, Yip CK, Sanowar S, Andre I, Kimbrough TG, Vuckovic M, Pfuetzner RA, Deng WY, Yu AC, Finlay
BB, Baker D, Miller SI, Strynadka NCJ. 2009. A Conserved Structural Motif Mediates Formation of the
Periplasmic Rings in the Type III Secretion System. Nature Structural & Molecular Biol. 16(5):468-476.
Sadreyev RI, Shi S, Baker D, Grishin NV. 2009. Structure Similarity Measure with Penalty for Close Nonequivalent Residues. Bioinformatics 25(10):1259-1263.
Zhu J, Luo BH, Barth P, Schonbrun J, Baker D, Springer TA. 2009. The Structure of a Receptor with Two
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Dietrich JA, Yoshikuni Y, Fisher KJ, Woolard FX, Ockey D, McPhee DJ, Renninger NS, Chang MCY, Baker D,
Keasling JD. 2009. A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered
Substrate-Promiscuous P450(BM3). ACS Chemical Biol. 4(4):261-267.
Muratore KE, Seeliger MA, Wang ZH, Fomina D, Neiswinger J, Havranek JJ, Baker D, Kuriyan J, Cole PA.
2009. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue. Biochemistry 48(15):33783386.
Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D. 2009. Alteration of Enzyme Specificity by
Computational Loop Remodeling and Design. Proc. Natl. Acad. Sci. USA 106(23):9215-9220.
Ashworth J, Baker D. 2009. Assessment of the Optimization of Affinity and Specificity at Protein DNA
Interfaces. Nucl. Acid Res. 37(10):e73.
Thyme SB, Jarjour J, Takeuchi, R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. 2009.
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Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Guentert P,
Herrmann T, Huang YJ, Jonker HRA, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der
Schot G, Vranken WF, Vuister GW, Bonvin AMJJ. 2009. CASD-NMR: Critical Assessment of Automated
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Davis IW, Raha K, Head MS, Baker D. 2009. Blind Docking of Pharmaceutically Relevant Compounds
Using RosettaLigand. Protein Science 18(9):1998-2002.
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Kim DE, Blum B, Bradley P, Baker D. 2009. Sampling Bottlenecks in De novo Protein Structure Prediction.
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Das R, Andre I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. 2009.
Simultaneous Prediction of Protein Folding and Docking at High Resolution. Proc. Natl. Acad. Sciences
USA 106(45):18978-18983.
Ban YA, Correia BE, Holmes M, Boni E, Sather N, Bretz C, Kalyuzhniy O, Xu C, Baker D, Stamatatos L,
Strong R, Schief W. 2009. 4e10 Epitope-Scaffolds Mimic the Antibody-Bound Epitope Conformation and
Block Neutralization By Sera From Rare HIV Plus Individuals. Retrovirology 6, Suppl. 3:P85.
Dosenovic P, Guenaga J, Ofek G, Baker D, Schief W, Kwong PD, Hedestam GBK, Wyatt RT. 2009. Analysis
of Antibody and B Cell Responses following Inoculation with computationally Designed HIV-1 2F5
Epitope Scaffold Proteins. Retrovirology 6, Suppl. 3:P178.
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L,
Sheffler W, Kim B-H, Das R, Grishin NV, Baker, D. 2009. Structure Prediction for CASP8 With All-Atom
refinement Using Rosetta. Proteins – Structure Function Bioinformatics 77, Suppl. 9:89-99.
Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. 2009. Improving Physical
Realism, Stereochemistry, and Side-Chain Accuracy in Homology Modeling: Four Approaches that
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303.
304.
305.
306.
307.
308.
309.
310.
311.
312.
Harger M, Zheng L, Moon A, Ager C, An JH, Choe C, Lai YL, Mo B, Zong D, Smith MD, Egbert RG, Mills JH,
Baker D, Pultz IS, Siegel JB. Expanding the product profile of a microbial alkane biosynthetic pathway.
ACS Synth Biol. 2013 Jan 18;2(1):59-62. doi: 10.1021/sb300061x. Epub 2012 Sep 26. PubMed PMID:
23656326
Nivon LG, Moretti R, Baker D. A Pareto-Optimal Refinement Method for Protein Design Scaffolds. Plos
One. Apr 2 2013;8(4).
Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D. Evolution of a designed retro-aldolase leads
to complete active site remodeling. Nat Chem Biol. 2013 Aug;9(8):494-8. doi: 10.1038/nchembio.1276.
Epub 2013 Jun 9. PubMed Central PMCID: PMC3720730.
Wang Y, Jarjour J, Boissel S, et al. Engineering an XID-Site Specific I-AniI Homing Endonuclease through
Combination of Rational Design and Directed Evolution. Molecular Therapy. Jun 2013;21:S122-S123.
Mintzer E, Jarjour J, Scharenberg A, et al. Development of Designer Homing Endonucleases for
Inactivation of the HIV Provirus. Molecular Therapy. Jun 2013;21:S73-S74
Molski MA, Goodman JL, Chou F-C, Baker D, Das R, Schepartz A. Remodeling a beta-peptide bundle.
Chemical Science. 2013;4(1):319-324
Leaver-Fay A, O'Meara MJ, Tyka M, et al. Scientific Benchmarks for Guiding Macromolecular Energy
Function Improvement. In: Keating AE, ed. Methods Enymol. 2013. Vol 523:109-143.
PMCID:PMC3724755.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM,
Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B,
Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, EsquivelRodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y,
Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H,
Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG,
Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang
SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting
the effect of mutations on protein-protein interactions. Proteins. 2013 Jul 10. [Epub ahead of print]
PubMed PMID: 23843247.
Kim DE, Dimaio F, Wang RY, Song Y, Baker D. One contact for every twelve residues allows robust and
accurate topology-level protein structure modeling. Proteins. 2013 Jul 31. doi: 10.1002/prot.24374.
[Epub ahead of print] PubMed PMID: 23900763.
van der Schot G, Zhang Z, Vernon R, Shen Y, Vranken WF, Baker D, Bonvin AM, Lange OF. Improving 3D
structure prediction from chemical shift data. J Biomol NMR. 2013 Sep;57(1):27-35. doi:
10.1007/s10858-013-9762-6. Epub 2013 Aug 3. PubMed PMID: 23912841
Vernon R, Shen Y, Baker D, Lange OF. Improved chemical shift based fragment selection for CS-Rosetta
using Rosetta3 fragment picker. J Biomol NMR. 2013 Aug 22. [Epub ahead of print] PubMed PMID:
23975356.
Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL,
Baker D. Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic
Level Accuracy. J Am Chem Soc. 2013 Aug 29. [Epub ahead of print] PubMed PMID: 23924187.
Shropshire TD, Reifert J, Rajagopalan S, Baker D, Feinstein SC, Daugherty PS. Amyloid β peptide cleavage
by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ mediated toxicity in vitro. Biol
Chem. 2013 Aug 30. [Epub ahead of print] PubMed PMID: 23989112.
Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF,
Tong L, Montelione GT, Baker D. Computational design of a protein-based enzyme inhibitor. J Mol Biol.
2013 Sep 23;425(18):3563-75. Epub 2013 Jul 1. PubMed PMID: 23827138. PMCID:PMC3818146
Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K,
Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity.
20
Revised 1/27/2015
313.
314.
315.
316.
317.
318.
319.
320.
321.
322.
323.
324.
325.
326.
327.
Nature. 2013 Sep 12;501 (7466):212-6. doi: 10.1038/nature12443. PubMed PMID:
24005320.PMCID:PMC3898436
Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact
predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):156749. doi: 10.1073/pnas.1314045110. Epub 2013 Sep 5. PubMed PMID: 24009338; PubMed Central PMCID:
PMC3785744.
Bjelic S, Kipnis Y, Wang L, Pianowski Z, Vorobiev S, Su M, Seetharaman J, Xiao R, Kornhaber G, Hunt JF,
Tong L, Hilvert D, Baker D. Exploration of Alternate Catalytic Mechanisms and Optimization Strategies
for Retroaldolase Design. J Mol Biol. 2013 Oct 23. pii: S0022-2836(13)00655-4. doi:
10.1016/j.jmb.2013.10.012. [Epub ahead of print] PubMed PMID: 24161950.
Nivón LG, Bjelic S, King C, Baker D. Automating human intuition for protein design. Proteins. 2013 Oct
30. doi: 10.1002/prot.24463. [Epub ahead of print] PubMed PMID: 24265170.
Cooper S, Khatib F, Baker D. Increasing public involvement in structural biology. Structure. 2013 Sep
3;21(9):1482-4. doi: 10.1016/j.str.2013.08.009. PubMed PMID: 24010706.
Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D. High-resolution
comparative modeling with RosettaCM. Structure. 2013 Oct 8;21(10):1735-42. doi:
10.1016/j.str.2013.08.005. Epub 2013 Sep 12. PubMed PMID: 24035711; PubMed Central PMCID:
PMC3811137. PMCID:PMC3811137
Cherny I, Greisen P Jr, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS. Engineering Vtype nerve agents detoxifying enzymes using computationally focused libraries. ACS Chem Biol. 2013
Nov 15;8(11):2394-403. doi: 10.1021/cb4004892. Epub 2013 Oct 4. PubMed PMID: 24041203.
DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution
crystallographic refinement with Phenix and Rosetta. Nat Methods. 2013 Nov;10(11):1102-4. doi:
10.1038/nmeth.2648. Epub 2013 Sep 29. PubMed PMID: 24076763.
Conway P, Tyka MD, Dimaio F, Konerding DE, Baker D. Relaxation of backbone bond geometry improves
protein energy landscape modeling. Protein Sci. 2013 Oct 29. doi: 10.1002/pro.2389. [Epub ahead of
print] PubMed PMID: 24265211. PMCID:PMC3892298
Thyme SB, Boissel SJ, Arshiya Quadri S, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J, Baker D.
Reprogramming homing endonuclease specificity through computational design and directed evolution.
Nucleic Acids Res. 2013 Nov 21. [Epub ahead of print] PubMed PMID: 24270794.
Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT,
Baker D, Scharenberg AM. megaTALs: a rare-cleaving nuclease architecture for therapeutic genome
engineering. Nucleic Acids Res. 2013 Nov 26. [Epub ahead of print] PubMed PMID: 24285304.
Fang J, Mehlich A, Koga N, Huang J, Koga R, Gao X, Hu C, Jin C, Rief M, Kast J, Baker D, Li H. Forced
protein unfolding leads to highly elastic and tough protein hydrogels. Nat Commun. 2013 Dec 19;4:2974.
doi: 10.1038/ncomms3974. PubMed PMID: 24352111.
Strauch EM, Fleishman SJ, Baker D. Computational design of a pH-sensitive IgG binding protein. Proc
Natl Acad Sci U S A. 2014 Jan 14;111(2):675-80. doi: 10.1073/pnas.1313605111. Epub 2013 Dec 31.
PubMed PMID: 24381156.PMCID:PMC3896196
Mao B, Tejero R, Baker D, Montelione GT. Protein NMR Structures Refined with Rosetta Have Higher
Accuracy Relative to Corresponding X-ray Crystal Structures. J Am Chem Soc. 2014 Jan 6. [Epub ahead of
print] PubMed PMID: 24392845.
Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB. Computationally designed libraries for
rapid enzyme stabilization. Protein Eng Des Sel. 2014 Jan 8. [Epub ahead of print] PubMed PMID:
24402331.PMCID:PMC3893934
Shropshire TD, Reifert J, Rajagopalan S, Baker D, Feinstein SC, Daugherty PS. Amyloid β peptide cleavage
by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. Biol
Chem. 2014 Jan 1;395(1):109-18. doi: 10.1515/hsz-2013-0230. PubMed PMID: 23989112.
21
Revised 1/27/2015
328.
329.
330.
331.
332.
333.
334.
335.
336.
337.
338.
339.
340.
Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal
V, Connell MJ, Stevens E, Schroeter A, Chen M, Macpherson S, Serra AM, Adachi Y, Holmes MA, Li Y,
Klevit RE, Graham BS, Wyatt RT, Baker D, Strong RK, Crowe JE, Johnson PR, Schief WR. Proof of principle
for epitope-focused vaccine design. Nature. 2014 Feb 5. doi: 10.1038/nature12966. [Epub ahead of
print] PubMed PMID: 24499818.
Thyme S, Baker D. Redesigning the Specificity of Protein-DNA Interactions with Rosetta. Methods Mol
Biol. 2014;1123:265-82. doi: 10.1007/978-1-62703-968-0_17. PubMed PMID: 24510272.
Liu Y, Tan YL, Zhang X, Bhabha G, Ekiert DC, Genereux JC, Cho Y, Kipnis Y, Bjelic S, Baker D, Kelly JW.
Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal
folding equilibrium shifts. Proc Natl Acad Sci U S A. 2014 Mar 3. [Epub ahead of print] PubMed PMID:
24591605.
Wang Y, Khan IF, Boissel S, Jarjour J, Pangallo J, Thyme S, Baker D, Scharenberg AM, Rawlings DJ.
Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked
immunodeficiency locus. Nucleic Acids Res. 2014 Mar 25. [Epub ahead of print] PubMed PMID:
24682825.
Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M,
Hunt JF, Cravatt BF, Baker D. Design of activated serine-containing catalytic triads with atomic-level
accuracy. Nat Chem Biol. 2014 Apr 6. doi: 10.1038/nchembio.1498. [Epub ahead of print] PubMed
PMID: 24705591.
Mazor R, Eberle JA, Hu X, Vassall AN, Onda M, Beers R, Lee EC, Kreitman RJ, Lee B, Baker D, King C,
Hassan R, Benhar I, Pastan I. Recombinant immunotoxin for cancer treatment with low immunogenicity
by identification and silencing of human T-cell epitopes. Proc Natl Acad Sci U S A. 2014 May 5. [Epub
ahead of print] PubMed PMID: 24799704.
Alushin GM, Lander GC, Kellogg EH, Zhang R, Baker D, Nogales E. High-Resolution Microtubule
Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis. Cell. 2014 May
22;157(5):1117-29. doi: 10.1016/j.cell.2014.03.053. PubMed PMID: 24855948.
Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D. Impact of scaffold
rigidity on the design and evolution of an artificial Diels-Alderase. Proc Natl Acad Sci U S A. 2014 May 20.
pii: 201401073. [Epub ahead of print] PubMed PMID: 24847076.
King C, Garza EN, Mazor R, Linehan JL, Pastan I, Pepper M, Baker D. Removing T-cell epitopes with
computational protein design. Proc Natl Acad Sci U S A. 2014 May 19. pii: 201321126. [Epub ahead of
print] PubMed PMID: 24843166.
King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D. Accurate design of
co-assembling multi-component protein nanomaterials. Nature. 2014 May 25. doi:
10.1038/nature13404. [Epub ahead of print] PubMed PMID: 24870237.
Magadán JG, Altman MO, Ince WL, Hickman HD, Stevens J, Chevalier A, Baker D, Wilson PC, Ahmed R,
Bennink JR, Yewdell JW. Biogenesis of influenza a virus hemagglutinin cross-protective stem epitopes.
PLoS Pathog. 2014 Jun 12;10(6):e1004204. doi: 10.1371/journal.ppat.1004204. eCollection 2014 Jun.
PubMed PMID: 24945804; PubMed Central PMCID: PMC4055778.
Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE,
Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, Baker D. A computationally
designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells. Cell. 2014 Jun
19;157(7):1644-56. doi: 10.1016/j.cell.2014.04.034. PubMed PMID: 24949974.
Magadán JG, Altman MO, Ince WL, Hickman HD, Stevens J, Chevalier A, Baker D, Wilson PC, Ahmed R,
Bennink JR, Yewdell JW. Biogenesis of influenza a virus hemagglutinin cross-protective stem epitopes.
PLoS Pathog. 2014 Jun 12;10(6):e1004204. doi: 10.1371/journal.ppat.1004204. eCollection 2014 Jun.
PubMed PMID: 24945804; PubMed Central PMCID: PMC4055778.
22
Revised 1/27/2015
341.
342.
343.
344.
345.
346.
347.
348.
Griss R, Schena A, Reymond L, Patiny L, Werner D, Tinberg CE, Baker D, Johnsson K. Bioluminescent
sensor proteins for point-of-care therapeutic drug monitoring. Nat Chem Biol. 2014 Jul;10(7):598-603.
doi: 10.1038/nchembio.1554. Epub 2014 Jun 8. PubMed PMID: 24907901.
Huang PS, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D.
High thermodynamic stability of parametrically designed helical bundles. Science. 2014 Oct
24;346(6208):481-5. doi: 10.1126/science.1257481. PubMed PMID: 25342806.
Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H,
Montelione GT, Hunt J, Baker D. A general computational approach for repeat protein design. J Mol Biol.
2015 Jan 30;427(2):563-75. doi: 10.1016/j.jmb.2014.11.005. Epub 2014 Nov 14. PubMed PMID:
25451037; PubMed Central PMCID: PMC4303030.
Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by
computational protein design. Nat Struct Mol Biol. 2015 Jan 12. doi: 10.1038/nsmb.2938. [Epub ahead
of print] PubMed PMID: 25580576.
Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG. Transition states.
Trapping a transition state in a computationally designed protein bottle. Science. 2015 Feb
20;347(6224):863-7. doi: 10.1126/science.aaa2424. PubMed PMID: 25700516.
Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. De novo protein
structure determination from near-atomic-resolution cryo-EM maps. Nat Methods. 2015 Feb 23. doi:
10.1038/nmeth.3287. [Epub ahead of print] PubMed PMID: 25707029.
DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits TC, Cheng Y, Baker D.
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local
refinement. Nat Methods. 2015 Feb 23. doi: 10.1038/nmeth.3286. [Epub ahead of print] PubMed PMID:
25707030.
Siegel JB, et al. Computational protein design enables a novel one-carbon assimilation pathway. Proc
Natl Acad Sci U S A. 2015 Mar 24;112(12):3704-9. doi: 10.1073/pnas.1500545112. Epub 2015 Mar 9.
PubMed PMID: 25775555; PubMed Central PMCID: PMC4378393.
Reviews
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
Baker D, Schekman R. 1989. Reconstitution of Protein Transport Using Broken Yeast Spheroplasts.
Methods Cell Biol 31:127-141.
Baker D, Shiau AK, Agard DA. 1993. The Role of Pro Regions in Protein Folding. Curr Opin Cell Biol
5(6):966-970.
Baker D, Agard DA. 1994. Influenza Hemagglutinin: Kinetic Control of Protein Function. Structure
2(10):907-910.
Baker D, Agard DA. 1994. Kinetics Versus Thermodynamics in Protein Folding. Biochemistry 33(24):75057509
Baker D. 1998. Metastable States and Folding Free Energy Barriers. Nature Structural Biology
5(12):1021-1024.
Plaxco KW, Riddle DS, Grantcharova V, Baker D. 1998. Simplified Proteins: Minimalist Solutions to the
'Protein Folding Problem'. Current Opinion in Structural Biology 8(1):80-85.
Alm E, Baker D. 1999. Matching Theory and Experiment in Protein Folding. Current Opinion in Structural
Biology 9(2):189-196.
Baker D, DeGrado WF. 1999. Engineering and Design. Curr Opin Struct Biol 9(4):485-486.
Baker D. 2000. A Surprising Simplicity to Protein Folding. Nature (London) 405(6782):39-42.
Baker D, Sali A. 2001. Protein Structure Prediction and Structural Genomics. Science 294(5540):93-96.
23
Revised 1/27/2015
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
Bonneau R, Baker D. 2001. Ab initio Protein Structure Prediction: Progress and Prospects. Annual Review
of Biophysics and Biomolecular Structure 30:173-189.
Fischer D, Baker D, Moult J. 2001. We Need Both Computer Models and Experiments. Nature
409(6820):558-558.
Grantcharova V, Alm EJ, Baker D, Horwich AL. 2001. Mechanisms of Protein Folding. Current Opinion in
Structural Biology 11(1):70-82.
Baker D, Lim WA. 2002. Folding and Binding - From Folding Towards Function - Editorial Overview.
Current Opinion in Structural Biology 12(1):11-13.
Schonbrun J, Wedemeyer WJ, Baker D. 2002. Protein Structure Prediction in 2002. Current Opinion in
Structural Biology 12(3):348-354.
Chivian D, Robertson T, Bonneau R, Baker D. 2003. Ab initio Methods. Methods Biochem Anal 44:547557.
Baker D, Eaton WA. 2004. Folding and Binding - Editorial Overview. Current Opinion in Structural Biology
14(1):67-69.
Bradley P, Kuhlman B, Dantas G, Baker D. 2004. Predicting Protein Structures Accurately - Response.
Science 304(5677):1596-1597.
Kortemme T, Baker D. 2004. Computational Design of Protein-Protein Interactions. Current Opinion in
Chemical Biology 8(1):91-97.
Kuhlman B, Baker D. 2004. Exploring Folding Free Energy Landscapes Using Computational Protein
Design. Current Opinion in Structural Biology 14(1):89-95.
Rohl CA, Strauss CE, Misura KM, Baker D. 2004. Protein Structure Prediction Using Rosetta. Methods
Enzymol 383:66-93.
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. 2005. Progress in Modeling of Protein
Structures and Interactions. Science 310(5748):638-642.
Advances in Protein Chemistry. In: Baldwin RL, Baker D, editors. Advances in Protein Chemistry: Elsevier
Academic Press Inc., 2006.
Baker D. 2006. Proteins by Design. Scientist 20(7):26-32.
Baker D, Group BF, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R.
2006. Engineering Life: Building a fab for Biology. Scientific American 294(6):44-51.
Baker D. 2006. Prediction and Design of Macromolecular Structures and Interactions. Philosophical
Transactions of the Royal Society B-Biological Sciences 361(1467):459-463.
Das R., Baker D. 2008. Macromolecular modeling with Rosetta. Annual Review of Biochemistry 77:363382.
Baker D. 2010. An Exciting but Challenging Road Ahead for Computational Enzyme Design. Protein
Science 19:1817-19.
Fleishman, S.J., Baker, D. 2012. Role of the biomolecular energy gap in protein design, structure, and
evolution. Cell 149:262-73. PMID:22500796
Whitehead, T.A., Baker, D., Fleishman, S.J. 2013. Computational design of novel protein binders and
experimental affinity maturation. Methods Enzymol. 423:1-19. PMID: 23422423
Adams, P.D., Baker, D., Brunger, A.T., Das, R, Dimaio, F., Read, R.J., Richardson, D.C., Richardson, J.S.,
Terwilliger, T.C. 2013. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta
Structural Biology Software Systems. Annu. Rev. Biophys. [Epub ahead of print] PMID: 23451892
Moal IH, Moretti R, Baker D, Fernández-Recio J. Scoring functions for protein-protein interactions. Curr
Opin Struct Biol. 2013 Jul 18. [Epub ahead of print] PubMed PMID: 23871100
Baker D. Centenary Award and Sir Frederick Gowland Hopkins Memorial Lecture. Protein folding,
structure prediction and design. Biochem Soc Trans. 2014 Apr;42(2):225-9. doi: 10.1042/BST20130055.
PubMed PMID: 24646222.
24
Revised 1/27/2015
Summary of Patents, Inventions, Licenses, and New Company Formation:
Patents (issued/applications): 7/55
Invention disclosures: 37 (10 since 2011)
Commercial Rosetta licensees: 27 (including J&J, Pfizer, Merck, Monsanto)
Rosetta@home participants: 356,578
Registered Foldit players: 334,672
Rosetta developers: ~360
Academic Rosetta licensees: ~9750
Countries using Rosetta: 94
Spinout companies: 4
Prospect Genomics (Genomics): Acquired by Eli Lilly
BioArchitecture Lab (Clean Energy): Partnerships with DuPont and BP, IP to Statoil
Arzeda (Agribusiness, Catalysts): Partnership with Dupont
Pregenen (Genome Engineering): Acquired by Bluebird Bio
Companies under translational research development at IPD: 2
PVP Biologics (Celiac Disease Therapy): Ingrid Swanson Pultz (Translational Investigator)
Cyrus Biotech (Rosetta SAS in the Cloud): Lucas Nivon (Translational Investigator)
Technology invented in the Baker lab has led to the formation of six companies, as follows.
Prospect Genomics: Founded in 1999 as a San Francisco based company focused on genomics and drug
discovery, acquired by Eli Lilly / Structural GenomiX in 2001.
BioArchitecture Lab: Founded in 2008 as a Seattle based company (relocated to Berkeley, CA in 2011) focused
on clean energy from kelp, in partnership with DuPont and BP; as of May 2013 no longer active, having licensed
their technology to Statoil.
ARZEDA: Founded in 2009 as a Seattle based company focused on enzyme engineering for agribusiness.
Pregenen: Founded in 2011 as a Seattle based company focused on engineering site directed nucleases for
genome engineering therapies; acquired in 2014 by Bluebird Bio (BLUE / NASDAQ).
PVP Biologics: Founded in 2012 as a Seattle based company (currently in incubation mode) focused on the
development of oral enzyme therapeutics for celiac disease, computationally designed enzymes that breakdown
gluten in the stomach.
Cyrus Biotech: Founded in 2014 as a Seattle based company (currently in incubation mode) commercializing a
user friendly Rosetta GUI for computational protein structure prediction and design; software as a service in the
cloud solution for biotechnology and pharmaceutical research.
25
Revised 1/27/2015
Patents:
Title
Filing Date
Application Patent #
Inventors
Method and System for
Optimization of Polymer
Sequences to Produce
Polymers with Stable, 3Dimensional
Conformations
1/26/2005
11/043,907
Patent
Issue Date
7,574,306 8/11/2009
David Baker, Brian
Kuhlman
MONOMERIC RED
FLUORESCENT PROTEINS
5/15/2007
11/748,641
7,671,185 3/2/2010
David Baker, Brooke Bevis,
Benjamin Glick, Michelle
Scalley-Kim, Daniel
Strongin
SYNTHETIC ENZYMES
DERIVED FROM
COMPUTATIONAL DESIGN
12/12/2008 12/334,360
8,340,951 12/25/2012 David Baker, Eric Althoff,
Daniela Grabs, Lin Jiang,
Andrew Wollacott,
Alexandre Zanghellini
STRUCTURE-BASED
DESIGN OF PEPTIDE
INHIBITORS OF AMYLOID
FIBRILLATION
2/8/2010
8,754,034 6/17/2014
David Baker, David
Eisenberg, John
Karanicolas, Stuart Sievers
ENZYME CATALYSTS FOR
DIELS-ALDER REACTIONS
12/14/2011 13/130,260
8,688,427 4/1/2014
David Baker, Justin Siegel,
Jennifer St. Clair,
Alexandre Zanghellini
POLYPEPTIDES FOR
TREATING AND/OR
LIMITING INFLUENZA
INFECTION
2/19/2013
13/813,356
8,765,686 7/1/2014
David Baker, Sarel
Fleishman, Timothy
Whitehead
ENZYME CATALYSTS FOR
DIELS-ALDER REACTIONS
12/14/2011 13/130,260
8,688,427 4/1/2014
David Baker, Justin Siegel,
Jennifer St. Clair,
Alexandre Zanghellini
12/702,175
26