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David Baker

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Protein Folding

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Publications

TOP 3
Joseph Jardine; Meaghan Jones; Jean-Philippe Julien; Oleksandr Kalyuzhniy; Skye MacPherson; John C Mathison; Andrew McGuire; Sergey Menis; David Nemazee; Travis Nieusma; Takayuki Ota; Devin Sok; Leonidas Stamatatos; Andrew B Ward; Ian A Wilson; David Baker; Dennis R Burton; Po-Ssu Huang; William R Schief
Rational HIV immunogen design to target specific germline B cell receptors.
Julien R C Bergeron; Frank Dimaio; Heather B Felise; Samuel I Miller; Richard A Pfuetzner; Nikolaos G Sgourakis; Marija Vuckovic; Liam J Worrall; Angel C Yu; David Baker; Natalie C J Strynadka
A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.
Matthew Harger; Yi-Ling Lai; Jeremy H Mills; Benjamin Mo; Austin Moon; Ingrid Swanson Pultz; Casey Ager; Ju Hye An; David Baker; Chris Choe; Robert G Egbert; Matthew D Smith; Lei Zheng; David Zong; Justin B Siegel
Expanding the product profile of a microbial alkane biosynthetic pathway.

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All Publications

2013: Joseph Jardine; Meaghan Jones; Jean-Philippe Julien; Oleksandr Kalyuzhniy; Skye MacPherson; John C Mathison; Andrew McGuire; Sergey Menis; David Nemazee; Travis Nieusma; Takayuki Ota; Devin Sok; Leonidas Stamatatos; Andrew B Ward; Ian A Wilson; David Baker; Dennis R Burton; Po-Ssu Huang; William R Schief
Rational HIV immunogen design to target specific germline B cell receptors.
Science (New York, N.Y.) 2013;340(6133):711-6.
2013: Julien R C Bergeron; Frank Dimaio; Heather B Felise; Samuel I Miller; Richard A Pfuetzner; Nikolaos G Sgourakis; Marija Vuckovic; Liam J Worrall; Angel C Yu; David Baker; Natalie C J Strynadka
A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.
PLoS pathogens 2013;9(4):e1003307.
2013: Matthew Harger; Yi-Ling Lai; Jeremy H Mills; Benjamin Mo; Austin Moon; Ingrid Swanson Pultz; Casey Ager; Ju Hye An; David Baker; Chris Choe; Robert G Egbert; Matthew D Smith; Lei Zheng; David Zong; Justin B Siegel
Expanding the product profile of a microbial alkane biosynthetic pathway.
ACS synthetic biology 2013;2(1):59-62.
2013: Lucas Gregorio Nivón; Rocco Moretti; David Baker
A pareto-optimal refinement method for protein design scaffolds.
PloS one 2013;8(4):e59004.
2013: Andrew Leaver-Fay; Sergey Lyskov; Matthew J O'Meara; Roland A Pache; Jane S Richardson; Jack Snoeyink; Yifan Song; James Thompson; Mike Tyka; David Baker; Ian W Davis; Jeffrey J Gray; James J Havranek; Ron Jacak; Elizabeth H Kellogg; Tanja Kortemme; Brian Kuhlman
Scientific benchmarks for guiding macromolecular energy function improvement.
Methods in enzymology 2013;523():109-43.
2012: Michael D Tyka; Kenneth Jung; David Baker
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.
Journal of computational chemistry 2012;33(31):2483-91.
2012: Nobuyasu Koga; Gaohua Liu; Gaetano T Montelione; Rie Tatsumi-Koga; Rong Xiao; Thomas B Acton; David Baker
Principles for designing ideal protein structures.
Nature 2012;491(7423):222-7.
2012: Florian Richter; Jayaraman Seetharaman; Adam J T Smith; Min Su; Liang Tong; Sergey Vorobiev; Rong Xiao; Rebecca Blomberg; Farhad Forouhar; Jasmine Gallaher; Alexej Grjasnow; Roger C Helgeson; Donald Hilvert; K N Houk; John F Hunt; Sagar D Khare; Gert Kiss; Gregory J Kornhaber; Alexandre P Kuzin; Scott Lew; Gaetano T Montelione; Zbigniew Pianowski; David Baker
Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.
Journal of the American Chemical Society 2012;134(39):16197-206.
2012: Yakov Kipnis; David Baker
Comparison of designed and randomly generated catalysts for simple chemical reactions.
Protein science : a publication of the Protein Society 2012;21(9):1388-95.
2012: Assaf Alon; David Baker; Frank DiMaio; Y Gat; Iris Grossman; Gilad Haran; Vamsi K Kodali; Tevie Mehlman; Colin Thorpe; Deborah Fass
The dynamic disulphide relay of quiescin sulphydryl oxidase.
Nature 2012;488(7411):414-8.
2012: Olga Khersonsky; Gert Kiss; Daniela Röthlisberger; Shira Albeck; David Baker; Orly Dym; Kendall N Houk; Dan S Tawfik
Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(26):10358-63.
2012: James M Thompson; Gaohua Liu; Jeffrey L Mills; Gaetano T Montelione; Paolo Rossi; Nikolaos G Sgourakis; Thomas Szyperski; Yuefeng Tang; David Baker
Accurate protein structure modeling using sparse NMR data and homologous structure information.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(25):9875-80.
2012: Summer B Thyme; David Baker; Philip Bradley
Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.
Journal of molecular biology 2012;419(3-4):255-74.
2012: Neil P King; Michael R Sawaya; William Sheffler; John P Sumida; Breanna S Vollmar; Todd O Yeates; Ingemar André; Tamir Gonen; David Baker
Computational design of self-assembling protein nanomaterials with atomic level accuracy.
Science (New York, N.Y.) 2012;336(6085):1171-4.
2012: Timothy A Whitehead; Ian A Wilson; Patrick Blair; Aaron Chevalier; Cecilia De Mattos; Cyrille Dreyfus; Sarel J Fleishman; Hetunandan Kamisetty; Chris A Myers; Yifan Song; David Baker
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.
Nature biotechnology 2012;30(6):543-8.
2012: Eric A Althoff; Lars Giger; Sanjay Hari; Daniel Herschlag; Donald Hilvert; Lin Jiang; Peter Kast; Jonathan K Lassila; Matthew Smith; Ling Wang; Zhizhi Wang; David Baker
Robust design and optimization of retroaldol enzymes.
Protein science : a publication of the Protein Society 2012;21(5):717-26.
2012: Wei Wu; Goran Ahlsen; David Baker; Lawrence Shapiro; S Lawrence Zipursky
Complementary chimeric isoforms reveal Dscam1 binding specificity in vivo.
Neuron 2012;74(2):261-8.
2012: Sarel J Fleishman; David Baker
Role of the biomolecular energy gap in protein design, structure, and evolution.
Cell 2012;149(2):262-73.
2012: Sagar D Khare; Yakov Kipnis; Haim Leader; Israel Silman; Yifan Song; Barry L Stoddard; Joel L Sussman; Ryo Takeuchi; Dan S Tawfik; Yacov Ashani; Jasmine L Gallaher; Moshe Goldsmith; Per Greisen; David Baker
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.
Nature chemical biology 2012;8(3):294-300.
2012: Ling Wang; Eric A Althoff; Jill Bolduc; Lars Giger; Donald Hilvert; Lin Jiang; Jonathan K Lassila; James Moody; Barry Stoddard; David Baker
Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
Journal of molecular biology 2012;415(3):615-25.
2011: Sarel J Fleishman; John Karanicolas; Eva-Maria Strauch; Timothy A Whitehead; Jacob E Corn; David Baker
Hotspot-centric de novo design of protein binders.
Journal of molecular biology 2011;413(5):1047-62.
2011: Miroslaw Gilski; David Baker; Seth Cooper; Frank DiMaio; Maciej Kazmierczyk; Firas Khatib; Szymon Krzywda; Iva Pichová; Zoran Popović; James Thompson; Helena Zábranská; Mariusz Jaskolski
High-resolution structure of a retroviral protease folded as a monomer.
Acta crystallographica. Section D, Biological crystallography 2011;67(Pt 11):907-14.
2011: Mihai L Azoitei; David Baker; Yih-En Andrew Ban; Chris Carrico; Lei Chen; Bruno E Correia; Po-Ssu Huang; Oleksandr Kalyuzhniy; Peter D Kwong; Jason S McLellan; Alexandria Schroeter; Roland K Strong; William R Schief
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Science (New York, N.Y.) 2011;334(6054):373-6.
2011: Firas Khatib; Szymon Krzywda; Iva Pichova; Zoran Popović; James Thompson; Helena Zabranska; Seth Cooper; Frank DiMaio; Miroslaw Gilski; Mariusz Jaskolski; Maciej Kazmierczyk; David Baker
Crystal structure of a monomeric retroviral protease solved by protein folding game players.
Nature structural & molecular biology 2011;18(10):1175-7.
2011: Lisa R Warner; Marcelo C Sousa; Krisztina Varga; David Baker; Susan L Baker; oliver lange; Arthur Pardi
Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set.
Journal of molecular biology 2011;411(1):83-95.
2011: James Thompson; David Baker
Incorporation of evolutionary information into Rosetta comparative modeling.
Proteins 2011;79(8):2380-8.
2011: Stuart A Sievers; Jason T Stevens; Anni Zhao; Onofrio Zirafi; David Baker; Howard W Chang; Lin Jiang; John Karanicolas; Jan Münch; David Eisenberg
Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.
Nature 2011;475(7354):96-100.
2011: Yifan Song; Michael Tyka; Andrew Leaver-Fay; James Thompson; David Baker
Structure-guided forcefield optimization.
Proteins 2011;79(6):1898-909.
2011: Frank DiMaio; Thomas C Terwilliger; Randy J Read; Alexander Wlodawer; Gustav Oberdorfer; Ulrike Wagner; Eugene Valkov; Assaf Alon; Deborah Fass; Herbert L Axelrod; Debanu Das; Sergey M Vorobiev; Hideo Iwaï; P Raj Pokkuluri; David Baker
Improved molecular replacement by density- and energy-guided protein structure optimization.
Nature 2011;473(7348):540-3.
2011: Sarel J Fleishman; Timothy A Whitehead; Damian C Ekiert; Cyrille Dreyfus; Jacob E Corn; Eva-Maria Strauch; Ian A Wilson; David Baker
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.
Science (New York, N.Y.) 2011;332(6031):816-21.
2011: Nikolaos G Sgourakis; oliver lange; Frank DiMaio; Ingemar André; Nicholas C Fitzkee; Paolo Rossi; Gaetano T Montelione; Ad Bax; David Baker
Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.
Journal of the American Chemical Society 2011;133(16):6288-98.
2011: John Karanicolas; Jacob E Corn; Irwin Chen; Lukasz A Joachimiak; Orly Dym; Sun H Peck; Shira Albeck; Tamar Unger; Wenxin Hu; Gaohua Liu; Scott Delbecq; David R Liu; Gaetano T Montelione; Clint P Spiegel; David Baker
A de novo protein binding pair by computational design and directed evolution.
Molecular cell 2011;42(2):250-60.
2011: Sarel J Fleishman; Sagar D Khare; Nobuyasu Koga; David Baker
Restricted sidechain plasticity in the structures of native proteins and complexes.
Protein science : a publication of the Protein Society 2011;20(4):753-7.
2011: Olga Khersonsky; Daniela Röthlisberger; Andrew M Wollacott; Paul Murphy; Orly Dym; Shira Albeck; Gert Kiss; Kendall N Houk; David Baker; Dan S Tawfik
Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution.
Journal of molecular biology 2011;407(3):391-412.
2011: Elizabeth H Kellogg; Andrew Leaver-Fay; David Baker
Role of conformational sampling in computing mutation-induced changes in protein structure and stability.
Proteins 2011;79(3):830-8.
2011: Michael D Tyka; Daniel A Keedy; Ingemar André; Frank Dimaio; Yifan Song; David C Richardson; Jane S Richardson; David Baker
Alternate states of proteins revealed by detailed energy landscape mapping.
Journal of molecular biology 2011;405(2):607-18.
2011: Po-Ssu Huang; Florian Richter; William R Schief; Robert Vernon; Ingemar Andre; Yih-En Andrew Ban; David Baker
RosettaRemodel: a generalized framework for flexible backbone protein design.
PloS one 2011;6(8):e24109.
2011: Frank DiMaio; Andrew Leaver-Fay; David Baker; Phil Bradley; Ingemar André
Modeling symmetric macromolecular structures in Rosetta3.
PloS one 2011;6(6):e20450.
2011: Sarel J Fleishman; Sagar D Khare; Nobuyasu Koga; Andrew Leaver-Fay; Gordon Lemmon; Jens Meiler; Paul Murphy; Florian Richter; Eva-Maria Strauch; Justin Ashworth; Jacob E Corn; David Baker
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.
PloS one 2011;6(6):e20161.
2011: Florian Richter; Andrew Leaver-Fay; Sagar D Khare; Sinisa Bjelic; David Baker
De novo enzyme design using Rosetta3.
PloS one 2011;6(5):e19230.
2010: Sarel J Fleishman; Jacob E Corn; Eva M Strauch; Tim A Whitehead; Ingemar Andre; James Thompson; James J Havranek; Rhiju Das; Philip Bradley; David Baker
Rosetta in CAPRI rounds 13-19.
Proteins 2010;78(15):3212-8.
2010: David Baker
An exciting but challenging road ahead for computational enzyme design.
Protein science : a publication of the Protein Society 2010;19(10):1817-9.
2010: William Sheffler; David Baker
RosettaHoles2: a volumetric packing measure for protein structure refinement and validation.
Protein science : a publication of the Protein Society 2010;19(10):1991-5.
2010: Bruno E Correia; Yih-En Andrew Ban; Margaret A Holmes; Hengyu Xu; Katharine Ellingson; Zane Kraft; Chris Carrico; Erica Boni; D Noah Sather; Camille Zenobia; Katherine Y Burke; Tyler Bradley-Hewitt; Jessica F Bruhn-Johannsen; Oleksandr Kalyuzhniy; David Baker; Roland K Strong; Leonidas Stamatatos; William R Schief
Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.
Structure (London, England : 1993) 2010;18(9):1116-26.
2010: Douglas M Fowler; Carlos L Araya; Sarel J Fleishman; Elizabeth H Kellogg; Jason J Stephany; David Baker; Stanley Fields
High-resolution mapping of protein sequence-function relationships.
Nature methods 2010;7(9):741-6.
2010: Gert Kiss; Daniela Röthlisberger; David Baker; Kendall N Houk
Evaluation and ranking of enzyme designs.
Protein science : a publication of the Protein Society 2010;19(9):1760-73.
2010: Justin B Siegel; Alexandre Zanghellini; Helena M Lovick; Gert Kiss; Abigail R Lambert; Jennifer L St Clair; Jasmine L Gallaher; Donald Hilvert; Michael H Gelb; Barry L Stoddard; Kendall N Houk; Forrest E Michael; David Baker
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
Science (New York, N.Y.) 2010;329(5989):309-13.
2010: Chu Wang; Robert Vernon; oliver lange; Michael Tyka; David Baker
Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.
Protein science : a publication of the Protein Society 2010;19(3):494-506.
2010: Srivatsan Raman; oliver lange; Paolo Rossi; Michael Tyka; Xu Wang; James Aramini; Gaohua Liu; Theresa A Ramelot; Alexander Eletsky; Thomas Szyperski; Michael A Kennedy; James H Prestegard; Gaetano T Montelione; David Baker
NMR structure determination for larger proteins using backbone-only data.
Science (New York, N.Y.) 2010;327(5968):1014-8.
2010: Srivatsan Raman; Yuanpeng J Huang; Binchen Mao; Paolo Rossi; James M Aramini; Gaohua Liu; Gaetano T Montelione; David Baker
Accurate automated protein NMR structure determination using unassigned NOESY data.
Journal of the American Chemical Society 2010;132(1):202-7.
2010: Sarah Sanowar; Pragya Singh; Richard A Pfuetzner; Ingemar André; Hongjin Zheng; Thomas Spreter; Natalie C J Strynadka; Tamir Gonen; David Baker; David R Goodlett; Samuel I Miller
Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system.
mBio 2010;1(3):.
2009: Rhiju Das; Ingemar André; Yang Shen; Yibing Wu; Alexander Lemak; Sonal Bansal; Cheryl H Arrowsmith; Thomas Szyperski; David Baker
Simultaneous prediction of protein folding and docking at high resolution.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(45):18978-83.
2009: Summer B Thyme; Jordan Jarjour; Ryo Takeuchi; James J Havranek; Justin Ashworth; Andrew M Scharenberg; Barry L Stoddard; David Baker
Exploitation of binding energy for catalysis and design.
Nature 2009;461(7268):1300-4.
2009: David E Kim; Ben Blum; Philip Bradley; David Baker
Sampling bottlenecks in de novo protein structure prediction.
Journal of molecular biology 2009;393(1):249-60.
2009: Frank DiMaio; Michael D Tyka; Matthew Baker; Wah Chiu; David Baker
Refinement of protein structures into low-resolution density maps using rosetta.
Journal of molecular biology 2009;392(1):181-90.
2009: Ian W Davis; Kaushik Raha; Martha S Head; David Baker
Blind docking of pharmaceutically relevant compounds using RosettaLigand.
Protein science : a publication of the Protein Society 2009;18(9):1998-2002.
2009: Paul M Murphy; Jill M Bolduc; Jasmine L Gallaher; Barry L Stoddard; David Baker
Alteration of enzyme specificity by computational loop remodeling and design.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(23):9215-20.
2009: James J Havranek; David Baker
Motif-directed flexible backbone design of functional interactions.
Protein science : a publication of the Protein Society 2009;18(6):1293-305.
2009: Justin Ashworth; David Baker
Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
Nucleic acids research 2009;37(10):e73.
2009: Ruslan I Sadreyev; ShuoYong Shi; David Baker; Nick V Grishin
Structure similarity measure with penalty for close non-equivalent residues.
Bioinformatics (Oxford, England) 2009;25(10):1259-63.
2009: Thomas Spreter; Calvin K Yip; Sarah Sanowar; Ingemar André; Tyler G Kimbrough; Marija Vuckovic; Richard A Pfuetzner; Wanyin Deng; Angel C Yu; B Brett Finlay; David Baker; Samuel I Miller; Natalie C J Strynadka
A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system.
Nature structural & molecular biology 2009;16(5):468-76.
2009: Jieqing Zhu; Bing-Hao Luo; Patrick Barth; Jack Schonbrun; David Baker; Timothy A Springer
The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3.
Molecular cell 2009;34(2):234-49.
2009: Theresa A Ramelot; Srivatsan Raman; Alexandre P Kuzin; Rong Xiao; Li-Chung Ma; Thomas B Acton; John F Hunt; Gaetano T Montelione; David Baker; Michael A Kennedy
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
Proteins 2009;75(1):147-67.
2009: P Barth; Björn Wallner; David Baker
Prediction of membrane protein structures with complex topologies using limited constraints.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(5):1409-14.
2009: Rhiju Das; David Baker
Prospects for de novo phasing with de novo protein models.
Acta crystallographica. Section D, Biological crystallography 2009;65(Pt 2):169-75.
2009: Ian W Davis; David Baker
RosettaLigand docking with full ligand and receptor flexibility.
Journal of molecular biology 2009;385(2):381-92.
2009: Srivatsan Raman; Robert Vernon; James Thompson; Michael Tyka; Ruslan Sadreyev; Jimin Pei; David Kim; Elizabeth Kellogg; Frank DiMaio; oliver lange; Lisa Kinch; Will Sheffler; Bong-Hyun Kim; Rhiju Das; Nick V Grishin; David Baker
Structure prediction for CASP8 with all-atom refinement using Rosetta.
Proteins 2009;77 Suppl 9():89-99.
2009: Will Sheffler; David Baker
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.
Protein science : a publication of the Protein Society 2009;18(1):229-39.
2008: Ingemar André; Charlie E M Strauss; David B Kaplan; Philip Bradley; David Baker
Emergence of symmetry in homooligomeric biological assemblies.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(42):16148-52.
2008: Michael Sawaya; Woj M Wojtowicz; Ingemar Andre; Bin Qian; Wei Wu; David Baker; David Eisenberg; S Lawrence Zipursky
A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.
Cell 2008;134(6):1007-18.
2008: Hyundae D Cho; Vanita D Sood; David Baker; Alan M Weiner
On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes.
RNA (New York, N.Y.) 2008;14(7):1284-9.
2008: Jian Qiu; Will Sheffler; David Baker; William Stafford Noble
Ranking predicted protein structures with support vector regression.
Proteins 2008;71(3):1175-82.
2008: Daniela Röthlisberger; Olga Khersonsky; Andrew M Wollacott; Lin Jiang; Jason DeChancie; Jamie Betker; Jasmine L Gallaher; Eric A Althoff; Alexandre Zanghellini; Orly Dym; Shira Albeck; Kendall N Houk; Dan S Tawfik; David Baker
Kemp elimination catalysts by computational enzyme design.
Nature 2008;453(7192):190-5.
2008: Lin Jiang; Eric A Althoff; Fernando R Clemente; Lindsey Doyle; Daniela Röthlisberger; Alexandre Zanghellini; Jasmine L Gallaher; Jamie L Betker; Fujie Tanaka; Carlos F Barbas; Donald Hilvert; Kendall N Houk; Barry L Stoddard; David Baker
De novo computational design of retro-aldol enzymes.
Science (New York, N.Y.) 2008;319(5868):1387-91.
2008: Christine McBeth; Audrey Seamons; Juan C Pizarro; Sarel J Fleishman; David Baker; Tanja Kortemme; Joan Goverman; Roland K Strong
A new twist in TCR diversity revealed by a forbidden alphabeta TCR.
Journal of molecular biology 2008;375(5):1306-19.
2007: Gil Goobes; Rivka Goobes; Joanna R Long; Jennifer M Popham; Vinodhkumar Raghunathan; Ora Schueler-Furman; Wendy J Shaw; Patrick S Stayton; David Baker; Charles T Campbell; James M Gibson; Gary P Drobny
The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite.
Magnetic resonance in chemistry : MRC 2007;45 Suppl 1():S32-47.
2007: Chu Wang; Ora Schueler-Furman; Ingemar Andre; Nir London; Sarel J Fleishman; Philip Bradley; Bin Qian; David Baker
RosettaDock in CAPRI rounds 6-12.
Proteins 2007;69(4):758-63.
2007: Bin Qian; Srivatsan Raman; Rhiju Das; Philip Bradley; Airlie J McCoy; Randy J Read; David Baker
High-resolution structure prediction and the crystallographic phase problem.
Nature 2007;450(7167):259-64.
2007: Ingemar André; Philip Bradley; Chu Wang; David Baker
Prediction of the structure of symmetrical protein assemblies.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(45):17656-61.
2007: Chu Wang; Philip Bradley; David Baker
Protein-protein docking with backbone flexibility.
Journal of molecular biology 2007;373(2):503-19.
2007: P Barth; Jack Schonbrun; David Baker
Toward high-resolution prediction and design of transmembrane helical protein structures.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(40):15682-7.
2007: Woj M Wojtowicz; Wei Wu; Ingemar Andre; Bin Qian; David Baker; S Lawrence Zipursky
A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains.
Cell 2007;130(6):1134-45.
2007: Rhiju Das; David Baker
Automated de novo prediction of native-like RNA tertiary structures.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(37):14664-9.
2007: Andriy S Yatsenko; Elizabeth E Gray; Halyna R Shcherbata; Larissa B Patterson; Vanita D Sood; Mariya M Kucherenko; David Baker; T. Hannele Ruohola-Baker
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.
The Journal of biological chemistry 2007;282(20):15159-69.
2007: Lars Malmström; Michael Riffle; Charlie E M Strauss; Dylan Chivian; Trisha Davis; Richard Bonneau; David Baker
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.
PLoS biology 2007;5(4):e76.
2007: Kiril Tsemekhman; Lukasz Goldschmidt; David Eisenberg; David Baker
Cooperative hydrogen bonding in amyloid formation.
Protein science : a publication of the Protein Society 2007;16(4):761-4.
2007: Gautam Dantas; Colin Corrent; Steve L Reichow; James J Havranek; Ziad M Eletr; Nancy G Isern; Brian Kuhlman; Gabriele Varani; Ethan A Merritt; David Baker
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design.
Journal of molecular biology 2007;366(4):1209-21.
2007: Alexander L Watters; Pritilekha Deka; Colin Corrent; David Callender; Gabriele Varani; Tobin R Sosnick; David Baker
The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
Cell 2007;128(3):613-24.
2007: Andrew M Wollacott; Alexandre Zanghellini; Paul Murphy; David Baker
Prediction of structures of multidomain proteins from structures of the individual domains.
Protein science : a publication of the Protein Society 2007;16(2):165-75.
2007: Halyna R Shcherbata; Andriy S Yatsenko; Larissa Patterson; Vanita D Sood; Uri Nudel; David Yaffe; David Baker; T. Hannele Ruohola-Baker
Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy.
The EMBO journal 2007;26(2):481-93.
2007: Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D Tyka; Divya Bhat; Dylan Chivian; David E Kim; William H Sheffler; Lars Malmström; Andrew M Wollacott; Chu Wang; Ingemar Andre; David Baker
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Proteins 2007;69 Suppl 8():118-28.
2006: Alexandre Zanghellini; Lin Jiang; Andrew M Wollacott; Gong Cheng; Jens Meiler; Eric A Althoff; Daniela Röthlisberger; David Baker
New algorithms and an in silico benchmark for computational enzyme design.
Protein science : a publication of the Protein Society 2006;15(12):2785-94.
2006: Philip Bradley; David Baker
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.
Proteins 2006;65(4):922-9.
2006: Gil Goobes; Rivka Goobes; Ora Schueler-Furman; David Baker; Patrick S Stayton; Gary P Drobny
Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(44):16083-8.
2006: Gautam Dantas; Alexander L Watters; Bradley M Lunde; Ziad M Eletr; Nancy G Isern; Toby Roseman; Jan Lipfert; Sebastian Doniach; Martin Tompa; Brian Kuhlman; Barry L Stoddard; Gabriele Varani; David Baker
Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.
Journal of molecular biology 2006;362(5):1004-24.
2006: Lukasz A Joachimiak; Tanja Kortemme; Barry L Stoddard; David Baker
Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.
Journal of molecular biology 2006;361(1):195-208.
2006: Justin Ashworth; James J Havranek; Carlos M Duarte; Django Sussman; Raymond J Monnat; Barry L Stoddard; David Baker
Computational redesign of endonuclease DNA binding and cleavage specificity.
Nature 2006;441(7093):656-9.
2006: Vladimir Yarov-Yarovoy; David Baker; William A Catterall
Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(19):7292-7.
2006: Neil Dobson; Gautam Dantas; David Baker; Gabriele Varani
High-resolution structural validation of the computational redesign of human U1A protein.
Structure (London, England : 1993) 2006;14(5):847-56.
2006: Kira M S Misura; Dylan Chivian; Carol A Rohl; David E Kim; David Baker
Physically realistic homology models built with ROSETTA can be more accurate than their templates.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(14):5361-6.
2006: Vanita D Sood; David Baker
Recapitulation and design of protein binding peptide structures and sequences.
Journal of molecular biology 2006;357(3):917-27.
2006: David Baker
Prediction and design of macromolecular structures and interactions.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1467):459-63.
2006: Alexandre V Morozov; Kiril Tsemekhman; David Baker
Electron density redistribution accounts for half the cooperativity of alpha helix formation.
The journal of physical chemistry. B 2006;110(10):4503-5.
2006: Michael J Thompson; Stuart A Sievers; John Karanicolas; Magdalena I Ivanova; David Baker; David Eisenberg
The 3D profile method for identifying fibril-forming segments of proteins.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(11):4074-8.
2006: Tracy Arakaki; Isolde Le Trong; Eric M Phizicky; Erin Quartley; George deTitta; Joseph Luft; Angela Lauricella; Lori Anderson; Oleksandr Kalyuzhniy; Elizabeth A Worthey; Peter J Myler; David Kim; David Baker; Wim G J Hol; Ethan A Merritt
Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major.
Acta crystallographica. Section F, Structural biology and crystallization communications 2006;62(Pt 3):175-9.
2006: Vladimir Yarov-Yarovoy; Jack Schonbrun; David Baker
Multipass membrane protein structure prediction using Rosetta.
Proteins 2006;62(4):1010-25.
2006: Dylan Chivian; David Baker
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection.
Nucleic acids research 2006;34(17):e112.
2005: Ora Schueler-Furman; Chu Wang; Philip Bradley; Kira M S Misura; David Baker
Progress in modeling of protein structures and interactions.
Science (New York, N.Y.) 2005;310(5748):638-42.
2005: Philip Bradley; Kira M S Misura; David Baker
Toward high-resolution de novo structure prediction for small proteins.
Science (New York, N.Y.) 2005;309(5742):1868-71.
2005: Ora Schueler-Furman; Chu Wang; David Baker
Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
Proteins 2005;60(2):187-94.
2005: Aaron Korkegian; Margaret E Black; David Baker; Barry L Stoddard
Computational thermostabilization of an enzyme.
Science (New York, N.Y.) 2005;308(5723):857-60.
2005: Chu Wang; Ora Schueler-Furman; David Baker
Improved side-chain modeling for protein-protein docking.
Protein science : a publication of the Protein Society 2005;14(5):1328-39.
2005: Jens Meiler; David Baker
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2005;173(2):310-6.
2005: Kira M S Misura; David Baker
Progress and challenges in high-resolution refinement of protein structure models.
Proteins 2005;59(1):15-29.
2005: Lin Jiang; Brian Kuhlman; Tanja Kortemme; David Baker
A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces.
Proteins 2005;58(4):893-904.
2005: Christopher T Saunders; David Baker
Recapitulation of protein family divergence using flexible backbone protein design.
Journal of molecular biology 2005;346(2):631-44.
2005: Gong Cheng; Bin Qian; R Samudrala; David Baker
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
Nucleic acids research 2005;33(18):5861-7.
2005: David E Kim; Dylan Chivian; Lars Malmström; David Baker
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.
Proteins 2005;61 Suppl 7():193-200.
2005: Dylan Chivian; David E Kim; Lars Malmström; Jack Schonbrun; Carol A Rohl; David Baker
Prediction of CASP6 structures using automated Robetta protocols.
Proteins 2005;61 Suppl 7():157-66.
2005: Philip Bradley; Lars Malmström; Bin Qian; Jack Schonbrun; Dylan Chivian; David E Kim; Jens Meiler; Kira M S Misura; David Baker
Free modeling with Rosetta in CASP6.
Proteins 2005;61 Suppl 7():128-34.
2004: James J Havranek; Carlos M Duarte; David Baker
A simple physical model for the prediction and design of protein-DNA interactions.
Journal of molecular biology 2004;344(1):59-70.
2004: Bin Qian; Angel R Ortiz; David Baker
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(43):15346-51.
2004: Kira M S Misura; Alexandre V Morozov; David Baker
Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction.
Journal of molecular biology 2004;342(2):651-64.
2004: David E Kim; Dylan Chivian; David Baker
Protein structure prediction and analysis using the Robetta server.
Nucleic acids research 2004;32(Web Server issue):W526-31.
2004: Jane Hitti; Lisa M Frenkel; Alice Stek; Sharon Nachman; David Baker; Adolfo Gonzalez-Garcia; Arthur Provisor; Edwin M Thorpe; Mary E Paul; Marc Foca; Jorge Gandia; Sharon Huang; Lee-Jen Wei; Laura M Stevens; D Heather Watts; James McNamara
Maternal toxicity with continuous nevirapine in pregnancy: results from PACTG 1022.
Journal of acquired immune deficiency syndromes (1999) 2004;36(3):772-6.
2004: Maximilian Schlosshauer; David Baker
Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness.
Protein science : a publication of the Protein Society 2004;13(6):1660-9.
2004: Carol A Rohl; Charlie E M Strauss; Dylan Chivian; David Baker
Modeling structurally variable regions in homologous proteins with rosetta.
Proteins 2004;55(3):656-77.
2004: Alexandre V Morozov; Tanja Kortemme; Kiril Tsemekhman; David Baker
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(18):6946-51.
2004: Alexander L Watters; David Baker
Searching for folded proteins in vitro and in silico.
European journal of biochemistry / FEBS 2004;271(9):1615-22.
2004: Michelle Scalley-Kim; David Baker
Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection.
Journal of molecular biology 2004;338(3):573-83.
2004: Tanja Kortemme; Lukasz A Joachimiak; Alex N Bullock; Aaron D Schuler; Barry L Stoddard; David Baker
Computational redesign of protein-protein interaction specificity.
Nature structural & molecular biology 2004;11(4):371-9.
2004: Krzysztof Ginalski; Leszek Rychlewski; David Baker; Nick V Grishin
Protein structure prediction for the male-specific region of the human Y chromosome.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(8):2305-10.
2004: Tanja Kortemme; David Baker
Computational design of protein-protein interactions.
Current opinion in chemical biology 2004;8(1):91-7.
2004: Yu Chen; Tanja Kortemme; Timothy Robertson; David Baker; Gabriele Varani
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys.
Nucleic acids research 2004;32(17):5147-62.
2004: Carol A Rohl; Charlie E M Strauss; Kira M S Misura; David Baker
Protein structure prediction using Rosetta.
Methods in enzymology 2004;383():66-93.
2003: Jens Meiler; David Baker
Rapid protein fold determination using unassigned NMR data.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(26):15404-9.
2003: Tony R Hazbun; Lars Malmström; Scott Anderson; Beth J Graczyk; Bethany Fox; Michael Riffle; Bryan A Sundin; J Derringer Aranda; W Hayes McDonald; Chun-Hwei Chiu; Brian E Snydsman; Philip Bradley; Eric G D Muller; Stanley Fields; David Baker; John R Yates; Trisha Davis
Assigning function to yeast proteins by integration of technologies.
Molecular cell 2003;12(6):1353-65.
2003: Brian Kuhlman; Gautam Dantas; Gregory C Ireton; Gabriele Varani; Barry L Stoddard; David Baker
Design of a novel globular protein fold with atomic-level accuracy.
Science (New York, N.Y.) 2003;302(5649):1364-8.
2003: William J Wedemeyer; David Baker
Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates.
Proteins 2003;53(2):262-72.
2003: Jens Meiler; David Baker
Coupled prediction of protein secondary and tertiary structure.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(21):12105-10.
2003: Ruslan I Sadreyev; David Baker; Nick V Grishin
Profile-profile comparisons by COMPASS predict intricate homologies between protein families.
Protein science : a publication of the Protein Society 2003;12(10):2262-72.
2003: Jerry Tsai; Richard Bonneau; Alexandre V Morozov; Brian Kuhlman; Carol A Rohl; David Baker
An improved protein decoy set for testing energy functions for protein structure prediction.
Proteins 2003;53(1):76-87.
2003: Gautam Dantas; Brian Kuhlman; David Callender; Michelle Wong; David Baker
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.
Journal of molecular biology 2003;332(2):449-60.
2003: Lisa N Kinch; David Baker; Nick V Grishin
Deciphering a novel thioredoxin-like fold family.
Proteins 2003;52(3):323-31.
2003: Jeffrey J Gray; Stewart Moughon; Chu Wang; Ora Schueler-Furman; Brian Kuhlman; Carol A Rohl; David Baker
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Journal of molecular biology 2003;331(1):281-99.
2003: Ora Schueler-Furman; David Baker
Conserved residue clustering and protein structure prediction.
Proteins 2003;52(2):225-35.
2003: Jeffrey J Gray; Stewart E Moughon; Tanja Kortemme; Ora Schueler-Furman; Kira M S Misura; Alexandre V Morozov; David Baker
Protein-protein docking predictions for the CAPRI experiment.
Proteins 2003;52(1):118-22.
2003: Benjamin J McFarland; Tanja Kortemme; Shuyuarn F Yu; David Baker; Roland K Strong
Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands.
Structure (London, England : 1993) 2003;11(4):411-22.
2003: Qian Yi; Ponni Rajagopal; Rachel E Klevit; David Baker
Structural and kinetic characterization of the simplified SH3 domain FP1.
Protein science : a publication of the Protein Society 2003;12(4):776-83.
2003: Tanja Kortemme; Alexandre V Morozov; David Baker
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.
Journal of molecular biology 2003;326(4):1239-59.
2003: Michelle Scalley-Kim; Philippe Minard; David Baker
Low free energy cost of very long loop insertions in proteins.
Protein science : a publication of the Protein Society 2003;12(2):197-206.
2003: Dylan Chivian; David E Kim; Lars Malmström; Philip Bradley; Timothy Robertson; Paul Murphy; Charlie E M Strauss; Richard Bonneau; Carol A Rohl; David Baker
Automated prediction of CASP-5 structures using the Robetta server.
Proteins 2003;53 Suppl 6():524-33.
2003: Philip Bradley; Dylan Chivian; Jens Meiler; Kira M S Misura; Carol A Rohl; William R Schief; William J Wedemeyer; Ora Schueler-Furman; Paul Murphy; Jack Schonbrun; Charlie E M Strauss; David Baker
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.
Proteins 2003;53 Suppl 6():457-68.
2003: Dylan Chivian; Timothy Robertson; Richard Bonneau; David Baker
Ab initio methods.
Methods of biochemical analysis 2003;44():547-57.
2002: Sehat Nauli; Brian Kuhlman; Isolde Le Trong; Ronald E Stenkamp; David C Teller; David Baker
Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2.
Protein science : a publication of the Protein Society 2002;11(12):2924-31.
2002: Tanja Kortemme; David Baker
A simple physical model for binding energy hot spots in protein-protein complexes.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(22):14116-21.
2002: Christopher T Saunders; David Baker
Evaluation of structural and evolutionary contributions to deleterious mutation prediction.
Journal of molecular biology 2002;322(4):891-901.
2002: Richard Bonneau; Charlie E M Strauss; Carol A Rohl; Dylan Chivian; Philip Bradley; Lars Malmström; Timothy Robertson; David Baker
De novo prediction of three-dimensional structures for major protein families.
Journal of molecular biology 2002;322(1):65-78.
2002: Richard Bonneau; Ingo Ruczinski; Jerry Tsai; David Baker
Contact order and ab initio protein structure prediction.
Protein science : a publication of the Protein Society 2002;11(8):1937-44.
2002: Ingo Ruczinski; Charles Kooperberg; Richard Bonneau; David Baker
Distributions of beta sheets in proteins with application to structure prediction.
Proteins 2002;48(1):85-97.
2002: Jack Schonbrun; William J Wedemeyer; David Baker
Protein structure prediction in 2002.
Current opinion in structural biology 2002;12(3):348-54.
2002: Bryan A Krantz; Alok K Srivastava; Sehat Nauli; David Baker; Robert T Sauer; Tobin R Sosnick
Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects.
Nature structural biology 2002;9(6):458-63.
2002: Carol A Rohl; David Baker
De novo determination of protein backbone structure from residual dipolar couplings using Rosetta.
Journal of the American Chemical Society 2002;124(11):2723-9.
2002: Brian Kuhlman; Jason W O'Neill; David E Kim; Kam Y J Zhang; David Baker
Accurate computer-based design of a new backbone conformation in the second turn of protein L.
Journal of molecular biology 2002;315(3):471-7.
2001: Jason W O'Neill; David E Kim; K Johnsen; David Baker; Kam Y J Zhang
Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus.
Structure (London, England : 1993) 2001;9(11):1017-27.
2001: David Baker; Andrej Sali
Protein structure prediction and structural genomics.
Science (New York, N.Y.) 2001;294(5540):93-6.
2001: Brian Kuhlman; Jason W O'Neill; David E Kim; Kam Y J Zhang; David Baker
Conversion of monomeric protein L to an obligate dimer by computational protein design.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10687-91.
2001: Sehat Nauli; Brian Kuhlman; David Baker
Computer-based redesign of a protein folding pathway.
Nature structural biology 2001;8(7):602-5.
2001: Richard Bonneau; Jerry Tsai; Ingo Ruczinski; David Baker
Functional inferences from blind ab initio protein structure predictions.
Journal of structural biology 2001;134(2-3):186-90.
2001: K M Kim; Eugene C Yi; David Baker; Kam Y J Zhang
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 2001;57(Pt 5):759-62.
2001: Jason W O'Neill; David E Kim; David Baker; Kam Y J Zhang
Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.
Acta crystallographica. Section D, Biological crystallography 2001;57(Pt 4):480-7.
2001: Richard Bonneau; Charlie E M Strauss; David Baker
Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.
Proteins 2001;43(1):1-11.
2001: VP Grantcharova; David Baker
Circularization changes the folding transition state of the src SH3 domain.
Journal of molecular biology 2001;306(3):555-63.
2001: Richard Bonneau; Jerry Tsai; Ingo Ruczinski; Dylan Chivian; Carol A Rohl; Charlie E M Strauss; David Baker
Rosetta in CASP4: progress in ab initio protein structure prediction.
Proteins 2001;Suppl 5():119-26.
2001: P Minard; Michelle Scalley-Kim; A Watters; David Baker
A "loop entropy reduction" phage-display selection for folded amino acid sequences.
Protein science : a publication of the Protein Society 2001;10(1):129-34.
2000: Kevin W Plaxco; Kim Simons; Ingo Ruczinski; David Baker
Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics.
Biochemistry 2000;39(37):11177-83.
2000: Brian Kuhlman; David Baker
Native protein sequences are close to optimal for their structures.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(19):10383-8.
2000: E L McCallister; Eric J Alm; David Baker
Critical role of beta-hairpin formation in protein G folding.
Nature structural biology 2000;7(8):669-73.
2000: Qian Yi; Michelle Scalley-Kim; Eric J Alm; David Baker
NMR characterization of residual structure in the denatured state of protein L.
Journal of molecular biology 2000;299(5):1341-51.
2000: VP Grantcharova; DS Riddle; David Baker
Long-range order in the src SH3 folding transition state.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(13):7084-9.
2000: David E Kim; C Fisher; David Baker
A breakdown of symmetry in the folding transition state of protein L.
Journal of molecular biology 2000;298(5):971-84.
2000: David Baker
A surprising simplicity to protein folding.
Nature 2000;405(6782):39-42.
2000: Kevin W Plaxco; S Larson; Ingo Ruczinski; DS Riddle; EC Thayer; B Buchwitz; A R Davidson; David Baker
Evolutionary conservation in protein folding kinetics.
Journal of molecular biology 2000;298(2):303-12.
2000: K Johnsen; Jason W O'Neill; David E Kim; David Baker; Kam Y J Zhang
Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus.
Acta crystallographica. Section D, Biological crystallography 2000;56(Pt 4):506-8.
2000: EC Thayer; C Bystroff; David Baker
Detection of protein coding sequences using a mixture model for local protein amino acid sequence.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):317-27.
1999: H Gu; N Doshi; David E Kim; Kim Simons; JV Santiago; Sehat Nauli; David Baker
Robustness of protein folding kinetics to surface hydrophobic substitutions.
Protein science : a publication of the Protein Society 1999;8(12):2734-41.
1999: ML Scalley; Sehat Nauli; ST Gladwin; David Baker
Structural transitions in the protein L denatured state ensemble.
Biochemistry 1999;38(48):15927-35.
1999: DS Riddle; VP Grantcharova; JV Santiago; Eric J Alm; Ingo Ruczinski; David Baker
Experiment and theory highlight role of native state topology in SH3 folding.
Nature structural biology 1999;6(11):1016-24.
1999: Eric J Alm; David Baker
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(20):11305-10.
1999: J Tsai; Michael Levitt; David Baker
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.
Journal of molecular biology 1999;291(1):215-25.
1999: Kevin W Plaxco; Ian S Millett; Daniel Segel; Sebastian Doniach; David Baker
Chain collapse can occur concomitantly with the rate-limiting step in protein folding.
Nature structural biology 1999;6(6):554-6.
1999: Eric J Alm; David Baker
Matching theory and experiment in protein folding.
Current opinion in structural biology 1999;9(2):189-96.
1999: Kim Simons; Richard Bonneau; Ingo Ruczinski; David Baker
Ab initio protein structure prediction of CASP III targets using ROSETTA.
Proteins 1999;Suppl 3():171-6.
1999: Kim Simons; Ingo Ruczinski; Charles Kooperberg; B A Fox; C Bystroff; David Baker
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.
Proteins 1999;34(1):82-95.
1998: David E Kim; Qian Yi; ST Gladwin; J M Goldberg; David Baker
The single helix in protein L is largely disrupted at the rate-limiting step in folding.
Journal of molecular biology 1998;284(3):807-15.
1998: Kevin W Plaxco; David Baker
Limited internal friction in the rate-limiting step of a two-state protein folding reaction.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(23):13591-6.
1998: David Shortle; Kim Simons; David Baker
Clustering of low-energy conformations near the native structures of small proteins.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(19):11158-62.
1998: C Bystroff; David Baker
Prediction of local structure in proteins using a library of sequence-structure motifs.
Journal of molecular biology 1998;281(3):565-77.
1998: VP Grantcharova; DS Riddle; JV Santiago; David Baker
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain.
Nature structural biology 1998;5(8):714-20.
1998: David E Kim; H Gu; David Baker
The sequences of small proteins are not extensively optimized for rapid folding by natural selection.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(9):4982-6.
1998: J A Rank; David Baker
Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water.
Biophysical chemistry 1998;71(2-3):199-204.
1998: Kevin W Plaxco; Kim Simons; David Baker
Contact order, transition state placement and the refolding rates of single domain proteins.
Journal of molecular biology 1998;277(4):985-94.
1998: Kevin W Plaxco; DS Riddle; VP Grantcharova; David Baker
Simplified proteins: minimalist solutions to the 'protein folding problem'.
Current opinion in structural biology 1998;8(1):80-5.
1998: Qian Yi; C Bystroff; Ponni Rajagopal; Rachel E Klevit; David Baker
Prediction and structural characterization of an independently folding substructure in the src SH3 domain.
Journal of molecular biology 1998;283(1):293-300.
1997: VP Grantcharova; David Baker
Folding dynamics of the src SH3 domain.
Biochemistry 1997;36(50):15685-92.
1997: H Gu; D Kim; David Baker
Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein.
Journal of molecular biology 1997;274(4):588-96.
1997: R Doyle; K Simons; H Qian; David Baker
Local interactions and the optimization of protein folding.
Proteins 1997;29(3):282-91.
1997: DS Riddle; JV Santiago; S T Bray-Hall; N Doshi; VP Grantcharova; Q Yi; David Baker
Functional rapidly folding proteins from simplified amino acid sequences.
Nature structural biology 1997;4(10):805-9.
1997: ML Scalley; David Baker
Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(20):10636-40.
1997: K F Han; C Bystroff; David Baker
Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns.
Protein science : a publication of the Protein Society 1997;6(7):1587-90.
1997: Kim Simons; Charles Kooperberg; E Huang; David Baker
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
Journal of molecular biology 1997;268(1):209-25.
1997: ML Scalley; Qian Yi; H Gu; A McCormack; J R Yates; David Baker
Kinetics of folding of the IgG binding domain of peptostreptococcal protein L.
Biochemistry 1997;36(11):3373-82.
1997: J A Rank; David Baker
A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding.
Protein science : a publication of the Protein Society 1997;6(2):347-54.
1997: C Bystroff; David Baker
Blind predictions of local protein structure in CASP2 targets using the I-sites library.
Proteins 1997;Suppl 1():167-71.
1997: Qian Yi; ML Scalley; Kim Simons; ST Gladwin; David Baker
Characterization of the free energy spectrum of peptostreptococcal protein L.
Folding & design 1997;2(5):271-80.
1996: C Bystroff; Kim Simons; K F Han; David Baker
Local sequence-structure correlations in proteins.
Current opinion in biotechnology 1996;7(4):417-21.
1996: K F Han; David Baker
Global properties of the mapping between local amino acid sequence and local structure in proteins.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(12):5814-8.
1996: Qian Yi; David Baker
Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR.
Protein science : a publication of the Protein Society 1996;5(6):1060-6.
1995: K F Han; David Baker
Recurring local sequence motifs in proteins.
Journal of molecular biology 1995;251(1):176-87.
1995: H Gu; Qian Yi; S T Bray; DS Riddle; A K Shiau; David Baker
A phage display system for studying the sequence determinants of protein folding.
Protein science : a publication of the Protein Society 1995;4(6):1108-17.
1993: David Baker; A K Shiau; David A Agard
The role of pro regions in protein folding.
Current opinion in cell biology 1993;5(6):966-70.
1992: David Baker; J L Silen; David A Agard
Protease pro region required for folding is a potent inhibitor of the mature enzyme.
Proteins 1992;12(4):339-44.