Username

Password

Preview

Sign-in free and Explore the Exciting World of BiomedExperts:

Over 1,800,000 Profiles
More than 3,500 Organizations worldwide
State of the Art Network Visualizations

Manage your own Profile
Locate Experts in your Country/Region
Locate Experts in your 1. and 2. Level Network
Connect to Experts Worldwide

NetworkView

David Baker

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.8 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Concepts & Ideas

Physiology

Protein Folding

Chemicals & Drugs

Activities & Behaviors

Occupations

Sign-in to see full Profile

Sign-in to see all Coauthors

Publications

TOP 3
Siegel Justin B; Zanghellini Alexandre; Lovick Helena M; Kiss Gert; Lambert Abigail R; St Clair Jennifer L; Gallaher Jasmine L; Hilvert Donald; Gelb Michael H; Stoddard Barry L; Houk Kendall N; Michael Forrest E; Baker David
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
Wang Chu; Vernon Robert; Lange Oliver; Tyka Michael; Baker David
Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.
Raman Srivatsan; Lange Oliver F; Rossi Paolo; Tyka Michael; Wang Xu; Aramini James; Liu Gaohua; Ramelot Theresa A; Eletsky Alexander; Szyperski Thomas; Kennedy Michael A; Prestegard James; Montelione Gaetano T; Baker David
NMR structure determination for larger proteins using backbone-only data.

Sign-in to see all Publications

Sign in free and see...

Visualized networks:

See your personal network in
sophisticated graphical views

GeoTargeted Searches:

Locate experts around the world
and connect with global collaborators

Research Profiles:

See the visualized research activity
of experts around the globe

Sign-in to see more

Geonetwork of David Baker (preview)

Cities where this author has publications
Cities where co-authors of this author have publications

Flash Player Required

Sign-in to see more

All Publications

2010: Siegel Justin B; Zanghellini Alexandre; Lovick Helena M; Kiss Gert; Lambert Abigail R; St Clair Jennifer L; Gallaher Jasmine L; Hilvert Donald; Gelb Michael H; Stoddard Barry L; Houk Kendall N; Michael Forrest E; Baker David
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
Science (New York, N.Y.) 2010;329(5989):309-13.
2010: Wang Chu; Vernon Robert; Lange Oliver; Tyka Michael; Baker David
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: Raman Srivatsan; Lange Oliver F; Rossi Paolo; Tyka Michael; Wang Xu; Aramini James; Liu Gaohua; Ramelot Theresa A; Eletsky Alexander; Szyperski Thomas; Kennedy Michael A; Prestegard James; Montelione Gaetano T; Baker David
NMR structure determination for larger proteins using backbone-only data.
Science (New York, N.Y.) 2010;327(5968):1014-8.
2010: Raman Srivatsan; Huang Yuanpeng J; Mao Binchen; Rossi Paolo; Aramini James M; Liu Gaohua; Montelione Gaetano T; Baker David
Accurate automated protein NMR structure determination using unassigned NOESY data.
Journal of the American Chemical Society 2010;132(1):202-7.
2009: Das Rhiju; André Ingemar; Shen Yang; Wu Yibing; Lemak Alexander; Bansal Sonal; Arrowsmith Cheryl H; Szyperski Thomas; Baker David
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: Thyme Summer B; Jarjour Jordan; Takeuchi Ryo; Havranek James J; Ashworth Justin; Scharenberg Andrew M; Stoddard Barry L; Baker David
Exploitation of binding energy for catalysis and design.
Nature 2009;461(7268):1300-4.
2009: Kim David E; Blum Ben; Bradley Philip; Baker David
Sampling bottlenecks in de novo protein structure prediction.
Journal of molecular biology 2009;393(1):249-60.
2009: DiMaio Frank; Tyka Michael D; Baker Matthew L; Chiu Wah; Baker David
Refinement of protein structures into low-resolution density maps using rosetta.
Journal of molecular biology 2009;392(1):181-90.
2009: Davis Ian W; Raha Kaushik; Head Martha S; Baker David
Blind docking of pharmaceutically relevant compounds using RosettaLigand.
Protein science : a publication of the Protein Society 2009;18(9):1998-2002.
2009: Murphy Paul M; Bolduc Jill M; Gallaher Jasmine L; Stoddard Barry L; Baker David
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: Ashworth Justin; Baker David
Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
Nucleic acids research 2009;37(10):e73.
2009: Havranek James J; Baker David
Motif-directed flexible backbone design of functional interactions.
Protein science : a publication of the Protein Society 2009;18(6):1293-305.
2009: Sadreyev Ruslan I; Shi ShuoYong; Baker David; Grishin Nick V
Structure similarity measure with penalty for close non-equivalent residues.
Bioinformatics (Oxford, England) 2009;25(10):1259-63.
2009: Spreter Thomas; Yip Calvin K; Sanowar Sarah; André Ingemar; Kimbrough Tyler G; Vuckovic Marija; Pfuetzner Richard A; Deng Wanyin; Yu Angel C; Finlay B Brett; Baker David; Miller Samuel I; Strynadka Natalie C J
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: Zhu Jieqing; Luo Bing-Hao; Barth Patrick; Schonbrun Jack; Baker David; Springer Timothy A
The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3.
Molecular cell 2009;34(2):234-49.
2009: Ramelot Theresa A; Raman Srivatsan; Kuzin Alexandre P; Xiao Rong; Ma Li-Chung; Acton Thomas B; Hunt John F; Montelione Gaetano T; Baker David; Kennedy Michael A
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
Proteins 2009;75(1):147-67.
2009: Barth P; Wallner B; Baker D
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: Das Rhiju; Baker David
Prospects for de novo phasing with de novo protein models.
Acta crystallographica. Section D, Biological crystallography 2009;65(Pt 2):169-75.
2009: Davis Ian W; Baker David
RosettaLigand docking with full ligand and receptor flexibility.
Journal of molecular biology 2009;385(2):381-92.
2009: Sheffler Will; Baker David
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.
2009: Raman Srivatsan; Vernon Robert; Thompson James; Tyka Michael; Sadreyev Ruslan; Pei Jimin; Kim David; Kellogg Elizabeth; DiMaio Frank; Lange Oliver; Kinch Lisa; Sheffler Will; Kim Bong-Hyun; Das Rhiju; Grishin Nick V; Baker David
Structure prediction for CASP8 with all-atom refinement using Rosetta.
Proteins 2009;77 Suppl 9():89-99.
2008: André Ingemar; Strauss Charlie E M; Kaplan David B; Bradley Philip; Baker David
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: Sawaya Michael R; Wojtowicz Woj M; Andre Ingemar; Qian Bin; Wu Wei; Baker David; Eisenberg David; Zipursky S Lawrence
A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.
Cell 2008;134(6):1007-18.
2008: Cho Hyundae D; Sood Vanita D; Baker David; Weiner Alan M
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: Röthlisberger Daniela; Khersonsky Olga; Wollacott Andrew M; Jiang Lin; DeChancie Jason; Betker Jamie; Gallaher Jasmine L; Althoff Eric A; Zanghellini Alexandre; Dym Orly; Albeck Shira; Houk Kendall N; Tawfik Dan S; Baker David
Kemp elimination catalysts by computational enzyme design.
Nature 2008;453(7192):190-5.
2008: Qiu Jian; Sheffler Will; Baker David; Noble William Stafford
Ranking predicted protein structures with support vector regression.
Proteins 2008;71(3):1175-82.
2008: Jiang Lin; Althoff Eric A; Clemente Fernando R; Doyle Lindsey; Röthlisberger Daniela; Zanghellini Alexandre; Gallaher Jasmine L; Betker Jamie L; Tanaka Fujie; Barbas Carlos F; Hilvert Donald; Houk Kendall N; Stoddard Barry L; Baker David
De novo computational design of retro-aldol enzymes.
Science (New York, N.Y.) 2008;319(5868):1387-91.
2008: McBeth Christine; Seamons Audrey; Pizarro Juan C; Fleishman Sarel J; Baker David; Kortemme Tanja; Goverman Joan M; Strong Roland K
A new twist in TCR diversity revealed by a forbidden alphabeta TCR.
Journal of molecular biology 2008;375(5):1306-19.
2007: Wang Chu; Schueler-Furman Ora; Andre Ingemar; London Nir; Fleishman Sarel J; Bradley Philip; Qian Bin; Baker David
RosettaDock in CAPRI rounds 6-12.
Proteins 2007;69(4):758-63.
2007: André Ingemar; Bradley Philip; Wang Chu; Baker David
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: Qian Bin; Raman Srivatsan; Das Rhiju; Bradley Philip; McCoy Airlie J; Read Randy J; Baker David
High-resolution structure prediction and the crystallographic phase problem.
Nature 2007;450(7167):259-64.
2007: Barth P; Schonbrun J; Baker D
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: Wang Chu; Bradley Philip; Baker David
Protein-protein docking with backbone flexibility.
Journal of molecular biology 2007;373(2):503-19.
2007: Wojtowicz Woj M; Wu Wei; Andre Ingemar; Qian Bin; Baker David; Zipursky S Lawrence
A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains.
Cell 2007;130(6):1134-45.
2007: Das Rhiju; Baker David
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: Yatsenko Andriy S; Gray Elizabeth E; Shcherbata Halyna R; Patterson Larissa B; Sood Vanita D; Kucherenko Mariya M; Baker David; Ruohola-Baker Hannele
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: Tsemekhman Kiril; Goldschmidt Lukasz; Eisenberg David; Baker David
Cooperative hydrogen bonding in amyloid formation.
Protein science : a publication of the Protein Society 2007;16(4):761-4.
2007: Malmström Lars; Riffle Michael; Strauss Charlie E M; Chivian Dylan; Davis Trisha N; Bonneau Richard; Baker David
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.
PLoS biology 2007;5(4):e76.
2007: Dantas Gautam; Corrent Colin; Reichow Steve L; Havranek James J; Eletr Ziad M; Isern Nancy G; Kuhlman Brian; Varani Gabriele; Merritt Ethan A; Baker David
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: Watters Alexander L; Deka Pritilekha; Corrent Colin; Callender David; Varani Gabriele; Sosnick Tobin; Baker David
The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
Cell 2007;128(3):613-24.
2007: Wollacott Andrew M; Zanghellini Alexandre; Murphy Paul; Baker David
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: Shcherbata Halyna R; Yatsenko Andriy S; Patterson Larissa; Sood Vanita D; Nudel Uri; Yaffe David; Baker David; Ruohola-Baker Hannele
Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy.
The EMBO journal 2007;26(2):481-93.
2007: Das Rhiju; Qian Bin; Raman Srivatsan; Vernon Robert; Thompson James; Bradley Philip; Khare Sagar; Tyka Michael D; Bhat Divya; Chivian Dylan; Kim David E; Sheffler William H; Malmström Lars; Wollacott Andrew M; Wang Chu; Andre Ingemar; Baker David
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Proteins 2007;69 Suppl 8():118-28.
2006: Zanghellini Alexandre; Jiang Lin; Wollacott Andrew M; Cheng Gong; Meiler Jens; Althoff Eric A; Röthlisberger Daniela; Baker David
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: Bradley Philip; Baker David
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.
Proteins 2006;65(4):922-9.
2006: Goobes Gil; Goobes Rivka; Schueler-Furman Ora; Baker David; Stayton Patrick S; Drobny Gary P
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: Dantas Gautam; Watters Alexander L; Lunde Bradley M; Eletr Ziad M; Isern Nancy G; Roseman Toby; Lipfert Jan; Doniach Sebastian; Tompa Martin; Kuhlman Brian; Stoddard Barry L; Varani Gabriele; Baker David
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: Joachimiak Lukasz A; Kortemme Tanja; Stoddard Barry L; Baker David
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: Ashworth Justin; Havranek James J; Duarte Carlos M; Sussman Django; Monnat Raymond J; Stoddard Barry L; Baker David
Computational redesign of endonuclease DNA binding and cleavage specificity.
Nature 2006;441(7093):656-9.
2006: Dobson Neil; Dantas Gautam; Baker David; Varani Gabriele
High-resolution structural validation of the computational redesign of human U1A protein.
Structure (London, England : 1993) 2006;14(5):847-56.
2006: Yarov-Yarovoy Vladimir; Baker David; Catterall William A
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: Misura Kira M S; Chivian Dylan; Rohl Carol A; Kim David E; Baker David
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: Thompson Michael J; Sievers Stuart A; Karanicolas John; Ivanova Magdalena I; Baker David; Eisenberg David
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: Morozov Alexandre V; Tsemekhman Kiril; Baker David
Electron density redistribution accounts for half the cooperativity of alpha helix formation.
The journal of physical chemistry. B 2006;110(10):4503-5.
2006: Baker David
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: Arakaki Tracy; Le Trong Isolde; Phizicky Eric; Quartley Erin; DeTitta George; Luft Joseph; Lauricella Angela; Anderson Lori; Kalyuzhniy Oleksandr; Worthey Elizabeth; Myler Peter J; Kim David; Baker David; Hol Wim G J; Merritt Ethan A
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: Sood Vanita D; Baker David
Recapitulation and design of protein binding peptide structures and sequences.
Journal of molecular biology 2006;357(3):917-27.
2006: Yarov-Yarovoy Vladimir; Schonbrun Jack; Baker David
Multipass membrane protein structure prediction using Rosetta.
Proteins 2006;62(4):1010-25.
2006: Chivian Dylan; Baker David
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection.
Nucleic acids research 2006;34(17):e112.
2005: Schueler-Furman Ora; Wang Chu; Bradley Phil; Misura Kira; Baker David
Progress in modeling of protein structures and interactions.
Science (New York, N.Y.) 2005;310(5748):638-42.
2005: Bradley Philip; Misura Kira M S; Baker David
Toward high-resolution de novo structure prediction for small proteins.
Science (New York, N.Y.) 2005;309(5742):1868-71.
2005: Schueler-Furman Ora; Wang Chu; Baker David
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: Korkegian Aaron; Black Margaret E; Baker David; Stoddard Barry L
Computational thermostabilization of an enzyme.
Science (New York, N.Y.) 2005;308(5723):857-60.
2005: Wang Chu; Schueler-Furman Ora; Baker David
Improved side-chain modeling for protein-protein docking.
Protein science : a publication of the Protein Society 2005;14(5):1328-39.
2005: Meiler Jens; Baker David
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: Misura Kira M S; Baker David
Progress and challenges in high-resolution refinement of protein structure models.
Proteins 2005;59(1):15-29.
2005: Jiang Lin; Kuhlman Brian; Kortemme Tanja; Baker David
A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces.
Proteins 2005;58(4):893-904.
2005: Saunders Christopher T; Baker David
Recapitulation of protein family divergence using flexible backbone protein design.
Journal of molecular biology 2005;346(2):631-44.
2005: Cheng Gong; Qian Bin; Samudrala Ram; Baker David
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: Kim David E; Chivian Dylan; Malmström Lars; Baker David
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.
Proteins 2005;61 Suppl 7():193-200.
2005: Chivian Dylan; Kim David E; Malmström Lars; Schonbrun Jack; Rohl Carol A; Baker David
Prediction of CASP6 structures using automated Robetta protocols.
Proteins 2005;61 Suppl 7():157-66.
2005: Bradley Philip; Malmström Lars; Qian Bin; Schonbrun Jack; Chivian Dylan; Kim David E; Meiler Jens; Misura Kira M S; Baker David
Free modeling with Rosetta in CASP6.
Proteins 2005;61 Suppl 7():128-34.
2004: Havranek James J; Duarte Carlos M; Baker David
A simple physical model for the prediction and design of protein-DNA interactions.
Journal of molecular biology 2004;344(1):59-70.
2004: Qian Bin; Ortiz Angel R; Baker David
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: Misura Kira M S; Morozov Alexandre V; Baker David
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: Kim David E; Chivian Dylan; Baker David
Protein structure prediction and analysis using the Robetta server.
Nucleic acids research 2004;32(Web Server issue):W526-31.
2004: Hitti Jane; Frenkel Lisa M; Stek Alice M; Nachman Sharon A; Baker David; Gonzalez-Garcia Adolfo; Provisor Arthur; Thorpe Edwin M; Paul Mary E; Foca Marc; Gandia Jorge; Huang Sharon; Wei Lee-Jen; Stevens Laura M; Watts D Heather; McNamara James;
Maternal toxicity with continuous nevirapine in pregnancy: results from PACTG 1022.
Journal of acquired immune deficiency syndromes (1999) 2004;36(3):772-6.
2004: Schlosshauer Maximilian; Baker David
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: Morozov Alexandre V; Kortemme Tanja; Tsemekhman Kiril; Baker David
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: Rohl Carol A; Strauss Charlie E M; Chivian Dylan; Baker David
Modeling structurally variable regions in homologous proteins with rosetta.
Proteins 2004;55(3):656-77.
2004: Watters Alexander L; Baker David
Searching for folded proteins in vitro and in silico.
European journal of biochemistry / FEBS 2004;271(9):1615-22.
2004: Scalley-Kim Michelle; Baker David
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: Kortemme Tanja; Joachimiak Lukasz A; Bullock Alex N; Schuler Aaron D; Stoddard Barry L; Baker David
Computational redesign of protein-protein interaction specificity.
Nature structural & molecular biology 2004;11(4):371-9.
2004: Kortemme Tanja; Baker David
Computational design of protein-protein interactions.
Current opinion in chemical biology 2004;8(1):91-7.
2004: Ginalski Krzysztof; Rychlewski Leszek; Baker David; Grishin Nick V
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: Chen Yu; Kortemme Tanja; Robertson Tim; Baker David; Varani Gabriele
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: Rohl Carol A; Strauss Charlie E M; Misura Kira M S; Baker David
Protein structure prediction using Rosetta.
Methods in enzymology 2004;383():66-93.
2003: Hazbun Tony R; Malmström Lars; Anderson Scott; Graczyk Beth J; Fox Bethany; Riffle Michael; Sundin Bryan A; Aranda J Derringer; McDonald W Hayes; Chiu Chun-Hwei; Snydsman Brian E; Bradley Phillip; Muller Eric G D; Fields Stanley; Baker David; Yates John R; Davis Trisha N
Assigning function to yeast proteins by integration of technologies.
Molecular cell 2003;12(6):1353-65.
2003: Meiler Jens; Baker David
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: Kuhlman Brian; Dantas Gautam; Ireton Gregory C; Varani Gabriele; Stoddard Barry L; Baker David
Design of a novel globular protein fold with atomic-level accuracy.
Science (New York, N.Y.) 2003;302(5649):1364-8.
2003: Wedemeyer William J; Baker David
Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates.
Proteins 2003;53(2):262-72.
2003: Meiler Jens; Baker David
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: Sadreyev Ruslan I; Baker David; Grishin Nick V
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: Tsai Jerry; Bonneau Richard; Morozov Alexandre V; Kuhlman Brian; Rohl Carol A; Baker David
An improved protein decoy set for testing energy functions for protein structure prediction.
Proteins 2003;53(1):76-87.
2003: Dantas Gautam; Kuhlman Brian; Callender David; Wong Michelle; Baker David
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: Gray Jeffrey J; Moughon Stewart; Wang Chu; Schueler-Furman Ora; Kuhlman Brian; Rohl Carol A; Baker David
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Journal of molecular biology 2003;331(1):281-99.
2003: Kinch Lisa N; Baker David; Grishin Nick V
Deciphering a novel thioredoxin-like fold family.
Proteins 2003;52(3):323-31.
2003: Schueler-Furman Ora; Baker David
Conserved residue clustering and protein structure prediction.
Proteins 2003;52(2):225-35.
2003: Gray Jeffrey J; Moughon Stewart E; Kortemme Tanja; Schueler-Furman Ora; Misura Kira M S; Morozov Alexandre V; Baker David
Protein-protein docking predictions for the CAPRI experiment.
Proteins 2003;52(1):118-22.
2003: McFarland Benjamin J; Kortemme Tanja; Yu Shuyuarn F; Baker David; Strong Roland K
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: Yi Qian; Rajagopal Ponni; Klevit Rachel E; Baker David
Structural and kinetic characterization of the simplified SH3 domain FP1.
Protein science : a publication of the Protein Society 2003;12(4):776-83.
2003: Kortemme Tanja; Morozov Alexandre V; Baker David
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: Scalley-Kim Michelle; Minard Philippe; Baker David
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: Chivian Dylan; Kim David E; Malmström Lars; Bradley Philip; Robertson Timothy; Murphy Paul; Strauss Charles E M; Bonneau Richard; Rohl Carol A; Baker David
Automated prediction of CASP-5 structures using the Robetta server.
Proteins 2003;53 Suppl 6():524-33.
2003: Bradley Philip; Chivian Dylan; Meiler Jens; Misura Kira M S; Rohl Carol A; Schief William R; Wedemeyer William J; Schueler-Furman Ora; Murphy Paul; Schonbrun Jack; Strauss Charles E M; Baker David
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.
Proteins 2003;53 Suppl 6():457-68.
2003: Chivian Dylan; Robertson Timothy; Bonneau Richard; Baker David
Ab initio methods.
Methods of biochemical analysis 2003;44():547-57.
2002: Nauli Sehat; Kuhlman Brian; Le Trong Isolde; Stenkamp Ronald E; Teller David; Baker David
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: Kortemme Tanja; Baker David
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: Saunders Christopher T; Baker David
Evaluation of structural and evolutionary contributions to deleterious mutation prediction.
Journal of molecular biology 2002;322(4):891-901.
2002: Bonneau Richard; Strauss Charlie E M; Rohl Carol A; Chivian Dylan; Bradley Phillip; Malmström Lars; Robertson Tim; Baker David
De novo prediction of three-dimensional structures for major protein families.
Journal of molecular biology 2002;322(1):65-78.
2002: Bonneau Richard; Ruczinski Ingo; Tsai Jerry; Baker David
Contact order and ab initio protein structure prediction.
Protein science : a publication of the Protein Society 2002;11(8):1937-44.
2002: Ruczinski Ingo; Kooperberg Charles; Bonneau Richard; Baker David
Distributions of beta sheets in proteins with application to structure prediction.
Proteins 2002;48(1):85-97.
2002: Schonbrun Jack; Wedemeyer William J; Baker David
Protein structure prediction in 2002.
Current opinion in structural biology 2002;12(3):348-54.
2002: Krantz Bryan A; Srivastava Alok K; Nauli Sehat; Baker David; Sauer Robert T; Sosnick Tobin R
Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects.
Nature structural biology 2002;9(6):458-63.
2002: Rohl Carol A; Baker David
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: Kuhlman Brian; O'Neill Jason W; Kim David E; Zhang Kam Y J; Baker David
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: O'Neill J W; Kim D E; Johnsen K; Baker D; Zhang K Y
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: Baker D; Sali A
Protein structure prediction and structural genomics.
Science (New York, N.Y.) 2001;294(5540):93-6.
2001: Kuhlman B; O'Neill J W; Kim D E; Zhang K Y; Baker D
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: Nauli S; Kuhlman B; Baker D
Computer-based redesign of a protein folding pathway.
Nature structural biology 2001;8(7):602-5.
2001: Bonneau R; Tsai J; Ruczinski I; Baker D
Functional inferences from blind ab initio protein structure predictions.
Journal of structural biology 2001;134(2-3):186-90.
2001: Kim K M; Yi E C; Baker D; Zhang K Y
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: O'Neill J W; Kim D E; Baker D; Zhang K Y
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: Bonneau R; Strauss C E; Baker D
Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.
Proteins 2001;43(1):1-11.
2001: Grantcharova V P; Baker D
Circularization changes the folding transition state of the src SH3 domain.
Journal of molecular biology 2001;306(3):555-63.
2001: Minard P; Scalley-Kim M; Watters A; Baker D
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.
2001: Bonneau R; Tsai J; Ruczinski I; Chivian D; Rohl C; Strauss C E; Baker D
Rosetta in CASP4: progress in ab initio protein structure prediction.
Proteins 2001;Suppl 5():119-26.
2000: Plaxco K W; Simons K T; Ruczinski I; Baker D
Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics.
Biochemistry 2000;39(37):11177-83.
2000: Kuhlman B; Baker D
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: McCallister E L; Alm E; Baker D
Critical role of beta-hairpin formation in protein G folding.
Nature structural biology 2000;7(8):669-73.
2000: Yi Q; Scalley-Kim M L; Alm E J; Baker D
NMR characterization of residual structure in the denatured state of protein L.
Journal of molecular biology 2000;299(5):1341-51.
2000: Grantcharova V P; Riddle D S; Baker D
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: Baker D
A surprising simplicity to protein folding.
Nature 2000;405(6782):39-42.
2000: Kim D E; Fisher C; Baker D
A breakdown of symmetry in the folding transition state of protein L.
Journal of molecular biology 2000;298(5):971-84.
2000: Plaxco K W; Larson S; Ruczinski I; Riddle D S; Thayer E C; Buchwitz B; Davidson A R; Baker D
Evolutionary conservation in protein folding kinetics.
Journal of molecular biology 2000;298(2):303-12.
2000: Johnsen K; O'Neill J W; Kim D E; Baker D; Zhang K Y
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: Thayer E C; Bystroff C; Baker D
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: Gu H; Doshi N; Kim D E; Simons K T; Santiago J V; Nauli S; Baker D
Robustness of protein folding kinetics to surface hydrophobic substitutions.
Protein science : a publication of the Protein Society 1999;8(12):2734-41.
1999: Scalley M L; Nauli S; Gladwin S T; Baker D
Structural transitions in the protein L denatured state ensemble.
Biochemistry 1999;38(48):15927-35.
1999: Riddle D S; Grantcharova V P; Santiago J V; Alm E; Ruczinski I; Baker D
Experiment and theory highlight role of native state topology in SH3 folding.
Nature structural biology 1999;6(11):1016-24.
1999: Alm E; Baker D
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: Tsai J; Levitt M; Baker D
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.
Journal of molecular biology 1999;291(1):215-25.
1999: Plaxco K W; Millett I S; Segel D J; Doniach S; Baker D
Chain collapse can occur concomitantly with the rate-limiting step in protein folding.
Nature structural biology 1999;6(6):554-6.
1999: Alm E; Baker D
Matching theory and experiment in protein folding.
Current opinion in structural biology 1999;9(2):189-96.
1999: Simons K T; Ruczinski I; Kooperberg C; Fox B A; Bystroff C; Baker D
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.
1999: Simons K T; Bonneau R; Ruczinski I; Baker D
Ab initio protein structure prediction of CASP III targets using ROSETTA.
Proteins 1999;Suppl 3():171-6.
1998: Kim D E; Yi Q; Gladwin S T; Goldberg J M; Baker D
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: Plaxco K W; Baker D
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: Shortle D; Simons K T; Baker D
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: Grantcharova V P; Riddle D S; Santiago J V; Baker D
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: Bystroff C; Baker D
Prediction of local structure in proteins using a library of sequence-structure motifs.
Journal of molecular biology 1998;281(3):565-77.
1998: Rank J A; Baker D
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: Kim D E; Gu H; Baker D
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: Plaxco K W; Simons K T; Baker D
Contact order, transition state placement and the refolding rates of single domain proteins.
Journal of molecular biology 1998;277(4):985-94.
1998: Plaxco K W; Riddle D S; Grantcharova V; Baker D
Simplified proteins: minimalist solutions to the 'protein folding problem'.
Current opinion in structural biology 1998;8(1):80-5.
1998: Yi Q; Bystroff C; Rajagopal P; Klevit R E; Baker D
Prediction and structural characterization of an independently folding substructure in the src SH3 domain.
Journal of molecular biology 1998;283(1):293-300.
1997: Gu H; Kim D; Baker D
Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein.
Journal of molecular biology 1997;274(4):588-96.
1997: Grantcharova V P; Baker D
Folding dynamics of the src SH3 domain.
Biochemistry 1997;36(50):15685-92.
1997: Doyle R; Simons K; Qian H; Baker D
Local interactions and the optimization of protein folding.
Proteins 1997;29(3):282-91.
1997: Riddle D S; Santiago J V; Bray-Hall S T; Doshi N; Grantcharova V P; Yi Q; Baker D
Functional rapidly folding proteins from simplified amino acid sequences.
Nature structural biology 1997;4(10):805-9.
1997: Scalley M L; Baker D
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: Han K F; Bystroff C; Baker D
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: Simons K T; Kooperberg C; Huang E; Baker D
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: Scalley M L; Yi Q; Gu H; McCormack A; Yates J R; Baker D
Kinetics of folding of the IgG binding domain of peptostreptococcal protein L.
Biochemistry 1997;36(11):3373-82.
1997: Rank J A; Baker D
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: Bystroff C; Baker D
Blind predictions of local protein structure in CASP2 targets using the I-sites library.
Proteins 1997;Suppl 1():167-71.
1997: Yi Q; Scalley M L; Simons K T; Gladwin S T; Baker D
Characterization of the free energy spectrum of peptostreptococcal protein L.
Folding & design 1997;2(5):271-80.
1996: Bystroff C; Simons K T; Han K F; Baker D
Local sequence-structure correlations in proteins.
Current opinion in biotechnology 1996;7(4):417-21.
1996: Yi Q; Baker D
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.
1996: Han K F; Baker D
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.
1995: Han K F; Baker D
Recurring local sequence motifs in proteins.
Journal of molecular biology 1995;251(1):176-87.
1995: Gu H; Yi Q; Bray S T; Riddle D S; Shiau A K; Baker D
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: Baker D; Shiau A K; Agard D A
The role of pro regions in protein folding.
Current opinion in cell biology 1993;5(6):966-70.
1992: Baker D; Silen J L; Agard D A
Protease pro region required for folding is a potent inhibitor of the mature enzyme.
Proteins 1992;12(4):339-44.

Sign-in to see more

Sign-in free and Explore the Exciting World of BiomedExperts:

NetworkView

David Baker

Research Profile (preview)

Concepts & Ideas

Physiology

Chemicals & Drugs

Activities & Behaviors

Occupations

Genes & Molecular Sequences

Procedures

Disorders

Phenomena

Network (preview)

Publications

Sign in free and see...

Visualized networks:

GeoTargeted Searches:

Research Profiles:

Geonetwork of David Baker (preview)

All Publications