2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 Earlier

Ashworth J, Baker D (2009). Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Res. 37, e73.

Barth P, Wallner B, Baker D (2009). Prediction of membrane protein structures with complex topologies using limited constraints. Proc. Natl. Acad. Sci. U.S.A. 106, 1409-14.

Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D (2009). Simultaneous prediction of protein folding and docking at high resolution. Proc. Natl. Acad. Sci. U.S.A. , .

Das R, Baker D (2009). Prospects for de novo phasing with de novo protein models. Acta Crystallogr. D Biol. Crystallogr. 65, 169-75.

Davis IW, Raha K, Head MS, Baker D (2009). Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Sci. 18, 1998-2002.

Davis IW, Baker D (2009). RosettaLigand docking with full ligand and receptor flexibility. J. Mol. Biol. 385, 381-92.

DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D (2009). Refinement of protein structures into low-resolution density maps using rosetta. J. Mol. Biol. 392, 181-90.

Havranek JJ, Baker D (2009). Motif-directed flexible backbone design of functional interactions. Protein Sci. 18, 1293-305.

Kidd BA, Baker D, Thomas WE (2009). Computation of conformational coupling in allosteric proteins. PLoS Comput. Biol. 5, e1000484.

Kim DE, Blum B, Bradley P, Baker D (2009). Sampling bottlenecks in de novo protein structure prediction. J. Mol. Biol. 393, 249-60.

Luo BH, Karanicolas J, Harmacek LD, Baker D, Springer TA (2009). Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. J. Biol. Chem. 284, 3917-24.

Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D (2009). Alteration of enzyme specificity by computational loop remodeling and design. Proc. Natl. Acad. Sci. U.S.A. 106, 9215-20.

Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA (2009). Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins 75, 147-67.

Sadreyev RI, Shi S, Baker D, Grishin NV (2009). Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics 25, 1259-63.

Sheffler W, Baker D (2009). RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci. 18, 229-39.

Shen Y, Vernon R, Baker D, Bax A (2009). De novo protein structure generation from incomplete chemical shift assignments. J. Biomol. NMR 43, 63-78.

Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D (2009). Exploitation of binding energy for catalysis and design. Nature 461, 1300-4.

Zhu J, Luo BH, Barth P, Schonbrun J, Baker D, Springer TA (2009). The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3. Mol. Cell 34, 234-49.

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Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL (2008). Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J. Am. Chem. Soc. 130, 15907-15.

André I, Strauss CE, Kaplan DB, Bradley P, Baker D (2008). Emergence of symmetry in homooligomeric biological assemblies. Proc. Natl. Acad. Sci. U.S.A. , .[Full Text PDF]

Cho HD, Sood VD, Baker D, Weiner AM (2008). On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes. RNA 14, 1284-9.[Full Text PDF]

Das R, Baker D (2008). Macromolecular modeling with rosetta. Annu. Rev. Biochem. 77, 363-82.[Full Text PDF]

Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D (2008). Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc. Natl. Acad. Sci. U.S.A. 105, 4144-9.

Fan E, Baker D, Fields S, Gelb MH, Buckner FS, Van Voorhis WC, Phizicky E, Dumont M, Mehlin C, Grayhack E, Sullivan M, Verlinde C, Detitta G, Meldrum DR, Merritt EA, Earnest T, Soltis M, Zucker F, Myler PJ, Schoenfeld L, Kim D, Worthey L, Lacount D, Vigna (2008). Structural genomics of pathogenic protozoa: an overview. Methods Mol. Biol. 426, 497-513.

Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM, Baker D, Campbell CT, Stayton PS, Drobny GP (2008). The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. 45, S32-S47.

Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D (2008). De novo computational design of retro-aldol enzymes. Science 319, 1387-91.

Keeble AH, Joachimiak LA, Maté MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C (2008). Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. J. Mol. Biol. 379, 745-59.

McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK (2008). A new twist in TCR diversity revealed by a forbidden alphabeta TCR. J. Mol. Biol. 375, 1306-19.

Qiu J, Sheffler W, Baker D, Noble WS (2008). Ranking predicted protein structures with support vector regression. Proteins 71, 1175-82.[Full Text PDF]

Raman S, Qian B, Baker D, Walker R C (2008). Advances in Rosetta protein structure prediction on massively parallel systems IBM J. Res. Dev. 52, 7-18.

Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D (2008). Kemp elimination catalysts by computational enzyme design. Nature 453, 190-5.[Full Text PDF]

Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL (2008). A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell 134, 1007-18.

Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008). Consistent blind protein structure generation from NMR chemical shift data. Proc. Natl. Acad. Sci. U.S.A. 105, 4685-90.

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André I, Bradley P, Wang C, Baker D (2007). Prediction of the structure of symmetrical protein assemblies. Proc. Natl. Acad. Sci. U.S.A. 104, 17656-61.[Full Text PDF]

Barth P, Schonbrun J, Baker D (2007). Toward high-resolution prediction and design of transmembrane helical protein structures. Proc. Natl. Acad. Sci. U.S.A. 104, 15682-7.

Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D (2007). High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J. Mol. Biol. 366, 1209-21.

Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D (2007). Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69 Suppl 8, 118-28.

Das R, Baker D (2007). Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A. 104, 14664-9.

Malmström L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D (2007). Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol. 5, e76.

Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D (2007). High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259-64.

Tsemekhman K, Goldschmidt L, Eisenberg D, Baker D (2007). Cooperative hydrogen bonding in amyloid formation. Protein Sci. 16, 761-4.[Full Text PDF]

Wang C, Bradley P, Baker D (2007). Protein-protein docking with backbone flexibility. J. Mol. Biol. 373, 503-19.

Wang C, Schueler-Furman O, Andre I, London N, Fleishman SJ, Bradley P, Qian B, Baker D (2007). RosettaDock in CAPRI rounds 6-12. Proteins 69, 758-63.

Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D (2007). The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell 128, 613-24.

Wojtowicz WM, Wu W, Andre I, Qian B, Baker D, Zipursky SL (2007). A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell 130, 1134-45.

Wollacott AM, Zanghellini A, Murphy P, Baker D (2007). Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci. 16, 165-75.

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Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D (2006). Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441, 656-9.[Full Text PDF]

Baker D (2006). Prediction and design of macromolecular structures and interactions. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 361, 459-63.[Full Text PDF]

Bradley P, Baker D (2006). Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 65, 922-9.

Chivian D, Baker D (2006). Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res. 34, e112.

Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D (2006). Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J. Mol. Biol. 362, 1004-24.

Dobson N, Dantas G, Baker D, Varani G (2006). High-resolution structural validation of the computational redesign of human U1A protein. Structure 14, 847-56.[Full Text PDF]

Joachimiak LA, Kortemme T, Stoddard BL, Baker D (2006). Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J. Mol. Biol. 361, 195-208.

Meiler J, Baker D (2006). ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65, 538-48.

Misura KM, Chivian D, Rohl CA, Kim DE, Baker D (2006). Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc. Natl. Acad. Sci. U.S.A. 103, 5361-6.

Morozov AV, Tsemekhman K, Baker D (2006). Electron density redistribution accounts for half the cooperativity of alpha helix formation. 110, 4503-5.[Full Text PDF]

Sood VD, Baker D (2006). Recapitulation and design of protein binding peptide structures and sequences. J. Mol. Biol. 357, 917-27.

Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D (2006). The 3D profile method for identifying fibril-forming segments of proteins. Proc. Natl. Acad. Sci. U.S.A. 103, 4074-8.

Yarov-Yarovoy V, Baker D, Catterall WA (2006). Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc. Natl. Acad. Sci. U.S.A. 103, 7292-7.[Full Text PDF]

Yarov-Yarovoy V, Schonbrun J, Baker D (2006). Multipass membrane protein structure prediction using Rosetta. Proteins 62, 1010-25.[Full Text PDF]

Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D (2006). New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 15, 2785-94.

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Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D (2005). Free modeling with Rosetta in CASP6. Proteins 61 Suppl 7, 128-34.[Full Text PDF]

Bradley P, Misura KM, Baker D (2005). Toward high-resolution de novo structure prediction for small proteins. Science 309, 1868-71.

Cheng G, Qian B, Samudrala R, Baker D (2005). Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res. 33, 5861-7.

Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D (2005). Prediction of CASP6 structures using automated Robetta protocols. Proteins 61 Suppl 7, 157-66.

Jiang L, Kuhlman B, Kortemme T, Baker D (2005). A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58, 893-904.

Kim DE, Chivian D, Malmström L, Baker D (2005). Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins 61 Suppl 7, 193-200.[Full Text PDF]

Meiler J, Baker D (2005). The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. J. Magn. Reson. 173, 310-6.

Misura KM, Baker D (2005). Progress and challenges in high-resolution refinement of protein structure models. Proteins 59, 15-29.

Morozov AV, Havranek JJ, Baker D, Siggia ED (2005). Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res. 33, 5781-98.[Full Text PDF]

Saunders CT, Baker D (2005). Recapitulation of protein family divergence using flexible backbone protein design. J. Mol. Biol. 346, 631-44.[Full Text PDF]

Schueler-Furman O, Wang C, Baker D (2005). Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 60, 187-94.

Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D (2005). Progress in modeling of protein structures and interactions. Science 310, 638-42.

Wang C, Schueler-Furman O, Baker D (2005). Improved side-chain modeling for protein-protein docking. Protein Sci. 14, 1328-39.

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Chen Y, Kortemme T, Robertson T, Baker D, Varani G (2004). A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res. 32, 5147-62.[Full Text PDF]

Havranek JJ, Duarte CM, Baker D (2004). A simple physical model for the prediction and design of protein-DNA interactions. J. Mol. Biol. 344, 59-70.[Full Text PDF]

Kim DE, Chivian D, Baker D (2004). Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32, W526-31.

Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D (2004). Computational redesign of protein-protein interaction specificity. Nat. Struct. Mol. Biol. 11, 371-9.

Kortemme T, Baker D (2004). Computational design of protein-protein interactions. 8, 91-7.

Kuhn M, Meiler J, Baker D (2004). Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins 54, 282-8.[Full Text PDF]

Misura KM, Morozov AV, Baker D (2004). Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J. Mol. Biol. 342, 651-64.

Morozov AV, Kortemme T, Tsemekhman K, Baker D (2004). Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc. Natl. Acad. Sci. U.S.A. 101, 6946-51.

Qian B, Ortiz AR, Baker D (2004). Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc. Natl. Acad. Sci. U.S.A. 101, 15346-51.

Rohl CA, Strauss CE, Misura KM, Baker D (2004). Protein structure prediction using Rosetta. Meth. Enzymol. 383, 66-93.[Full Text PDF]

Rohl CA, Strauss CE, Chivian D, Baker D (2004). Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55, 656-77.[Full Text PDF]

Scalley-Kim M, Baker D (2004). Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J. Mol. Biol. 338, 573-83.[Full Text PDF]

Schlosshauer M, Baker D (2004). Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci. 13, 1660-9.[Full Text PDF]

Svensson HG, Wedemeyer WJ, Ekstrom JL, Callender DR, Kortemme T, Kim DE, Sjöbring U, Baker D (2004). Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry 43, 2445-57.[Full Text PDF]

Watters AL, Baker D (2004). Searching for folded proteins in vitro and in silico. Eur. J. Biochem. 271, 1615-22.[Full Text PDF]

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Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D (2003). Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins 53 Suppl 6, 457-68.

Chivian D, Robertson T, Bonneau R, Baker D (2003). Ab initio methods. 44, 547-57.

Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D (2003). Automated prediction of CASP-5 structures using the Robetta server. Proteins 53 Suppl 6, 524-33.[Full Text PDF]

Dantas G, Kuhlman B, Callender D, Wong M, Baker D (2003). A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J. Mol. Biol. 332, 449-60.

Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D (2003). Protein-protein docking predictions for the CAPRI experiment. Proteins 52, 118-22.

Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003). Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331, 281-99.

Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV (2003). Contact order revisited: influence of protein size on the folding rate. Protein Sci. 12, 2057-62.[Full Text PDF]

Kortemme T, Morozov AV, Baker D (2003). An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326, 1239-59.

Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003). Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364-8.

McFarland BJ, Kortemme T, Yu SF, Baker D, Strong RK (2003). Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure 11, 411-22.[Full Text PDF]

Meiler J, Baker D (2003). Coupled prediction of protein secondary and tertiary structure. Proc. Natl. Acad. Sci. U.S.A. 100, 12105-10.

Meiler J, Baker D (2003). Rapid protein fold determination using unassigned NMR data. Proc. Natl. Acad. Sci. U.S.A. 100, 15404-9.

Millet O, Mittermaier A, Baker D, Kay LE (2003). The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. J. Mol. Biol. 329, 551-63.[Full Text PDF]

A. Morozov, T. Kortemme,D. Baker (2003). Evaluation of Models of Electrostatic Interactions in Proteins J. Phys. Chem. B 107, 2075-2090.

Scalley-Kim M, Minard P, Baker D (2003). Low free energy cost of very long loop insertions in proteins. Protein Sci. 12, 197-206.[Full Text PDF]

Schueler-Furman O, Baker D (2003). Conserved residue clustering and protein structure prediction. Proteins 52, 225-35.

Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D (2003). An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53, 76-87.[Full Text PDF]

Wedemeyer WJ, Baker D (2003). Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins 53, 262-72.[Full Text PDF]

Yi Q, Rajagopal P, Klevit RE, Baker D (2003). Structural and kinetic characterization of the simplified SH3 domain FP1. Protein Sci. 12, 776-83.

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Alm E, Morozov AV, Kortemme T, Baker D (2002). Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 322, 463-76.[Full Text PDF]

Bonneau R, Ruczinski I, Tsai J, Baker D (2002). Contact order and ab initio protein structure prediction. Protein Sci. 11, 1937-44.

Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D (2002). De novo prediction of three-dimensional structures for major protein families. J. Mol. Biol. 322, 65-78.

Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL (2002). Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell 10, 895-905.[Full Text PDF]

Kortemme T, Baker D (2002). A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. U.S.A. 99, 14116-21.

Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR (2002). Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nat. Struct. Biol. 9, 458-63.[Full Text PDF]

Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW (2002). Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. J. Mol. Biol. 316, 225-33.[Full Text PDF]

Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D (2002). Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein Sci. 11, 2924-31.

Rohl CA, Baker D (2002). De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J. Am. Chem. Soc. 124, 2723-9.

Ruczinski I, Kooperberg C, Bonneau R, Baker D (2002). Distributions of beta sheets in proteins with application to structure prediction. Proteins 48, 85-97.

Saunders CT, Baker D (2002). Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J. Mol. Biol. 322, 891-901.[Full Text PDF]

Maximillian Schlosshauer,D. Baker (2002). A General Expression for Bimolecular Association Rates with Orientational Constraints J. Phys. Chem. B 106, 12079-12083.

Schonbrun J, Wedemeyer WJ, Baker D (2002). Protein structure prediction in 2002. Curr. Opin. Struct. Biol. 12, 348-54.

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Baker D, Sali A (2001). Protein structure prediction and structural genomics. Science 294, 93-6.[Full Text PDF]

Bonneau R, Strauss CE, Baker D (2001). Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins 43, 1-11.

Bonneau R, Baker D (2001). Ab initio protein structure prediction: progress and prospects. 30, 173-89.

Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D (2001). Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins Suppl 5, 119-26.[Full Text PDF]

Bonneau R, Tsai J, Ruczinski I, Baker D (2001). Functional inferences from blind ab initio protein structure predictions. J. Struct. Biol. 134, 186-90.

Grantcharova V, Alm EJ, Baker D, Horwich AL (2001). Mechanisms of protein folding. Curr. Opin. Struct. Biol. 11, 70-82.[Full Text PDF]

Grantcharova VP, Baker D (2001). Circularization changes the folding transition state of the src SH3 domain. J. Mol. Biol. 306, 555-63.

Kim KM, Yi EC, Baker D, Zhang KY (2001). Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase. Acta Crystallogr. D Biol. Crystallogr. 57, 759-62.[Full Text PDF]

Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D (2001). Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc. Natl. Acad. Sci. U.S.A. 98, 10687-91.

Lee MR, Tsai J, Baker D, Kollman PA (2001). Molecular dynamics in the endgame of protein structure prediction. J. Mol. Biol. 313, 417-30.[Full Text PDF]

Lee MR, Baker D, Kollman PA (2001). 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. J. Am. Chem. Soc. 123, 1040-6.[Full Text PDF]

Minard P, Scalley-Kim M, Watters A, Baker D (2001). A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein Sci. 10, 129-34.

Nauli S, Kuhlman B, Baker D (2001). Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 8, 602-5.

J. W. O'Neill, D. E. Kim, D. Baker,K. Y. Zhang (2001). Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution Acta Crystallogr D Biol Crystallogr 57, 480-7.

J. W. O'Neill, D. E. Kim, K. Johnsen, D. Baker,K. Y. Zhang (2001). Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus Structure (Camb) 9, 1017-27.

Simons KT, Strauss C, Baker D (2001). Prospects for ab initio protein structural genomics. J. Mol. Biol. 306, 1191-9.[Full Text PDF]

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Baker D (2000). A surprising simplicity to protein folding. Nature 405, 39-42.

Bowers PM, Strauss CE, Baker D (2000). De novo protein structure determination using sparse NMR data. J. Biomol. NMR 18, 311-8.

Bystroff C, Thorsson V, Baker D (2000). HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J. Mol. Biol. 301, 173-90.[Full Text PDF]

Grantcharova VP, Riddle DS, Baker D (2000). Long-range order in the src SH3 folding transition state. Proc. Natl. Acad. Sci. U.S.A. 97, 7084-9.

Kim DE, Fisher C, Baker D (2000). A breakdown of symmetry in the folding transition state of protein L. J. Mol. Biol. 298, 971-84.

Kuhlman B, Baker D (2000). Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. U.S.A. 97, 10383-8.

McCallister EL, Alm E, Baker D (2000). Critical role of beta-hairpin formation in protein G folding. Nat. Struct. Biol. 7, 669-73.

Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D (2000). Evolutionary conservation in protein folding kinetics. J. Mol. Biol. 298, 303-12.

Thayer EC, Bystroff C, Baker D (2000). Detection of protein coding sequences using a mixture model for local protein amino acid sequence. J. Comput. Biol. 7, 317-27.

Yi Q, Scalley-Kim ML, Alm EJ, Baker D (2000). NMR characterization of residual structure in the denatured state of protein L. J. Mol. Biol. 299, 1341-51.

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Alm E, Baker D (1999). Matching theory and experiment in protein folding. Curr. Opin. Struct. Biol. 9, 189-96.

Alm E, Baker D (1999). Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. U.S.A. 96, 11305-10.

Baker D, DeGrado WF (1999). Engineering and design 9, 485-6.

Gu H, Doshi N, Kim DE, Simons KT, Santiago JV, Nauli S, Baker D (1999). Robustness of protein folding kinetics to surface hydrophobic substitutions. Protein Sci. 8, 2734-41.

Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D (1999). Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat. Struct. Biol. 6, 554-6.

Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D (1999). Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 6, 1016-24.

Scalley ML, Nauli S, Gladwin ST, Baker D (1999). Structural transitions in the protein L denatured state ensemble. Biochemistry 38, 15927-35.

Simons KT, Bonneau R, Ruczinski I, Baker D (1999). Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl 3, 171-6.

Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D (1999). Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34, 82-95.

Tsai J, Levitt M, Baker D (1999). Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J. Mol. Biol. 291, 215-25.

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Baker D (1998). Metastable states and folding free energy barriers. Nat. Struct. Biol. 5, 1021-4.[Full Text PDF]

Bystroff C, Baker D (1998). Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol. 281, 565-77.

Grantcharova VP, Riddle DS, Santiago JV, Baker D (1998). Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat. Struct. Biol. 5, 714-20.

Kim DE, Gu H, Baker D (1998). The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proc. Natl. Acad. Sci. U.S.A. 95, 4982-6.

Kim DE, Yi Q, Gladwin ST, Goldberg JM, Baker D (1998). The single helix in protein L is largely disrupted at the rate-limiting step in folding. J. Mol. Biol. 284, 807-15.

Plaxco KW, Simons KT, Baker D (1998). Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985-94.

Plaxco KW, Riddle DS, Grantcharova V, Baker D (1998). Simplified proteins: minimalist solutions to the 'protein folding problem'. Curr. Opin. Struct. Biol. 8, 80-5.

Plaxco KW, Baker D (1998). Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proc. Natl. Acad. Sci. U.S.A. 95, 13591-6.

Rank JA, Baker D (1998). Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water. Biophys. Chem. 71, 199-204.

Shortle D, Simons KT, Baker D (1998). Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. U.S.A. 95, 11158-62.

Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D (1998). Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J. Mol. Biol. 283, 293-300.

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Han KF, Bystroff C, Baker D (1997). Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Sci. 6, 1587-90.[Full Text PDF]

Rank JA, Baker D (1997). A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding. Protein Sci. 6, 347-54.

Scalley ML, Yi Q, Gu H, McCormack A, Yates JR, Baker D (1997). Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Biochemistry 36, 3373-82.

Gu H, Kim D, Baker D (1997). Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. J. Mol. Biol. 274, 588-96.

Grantcharova VP, Baker D (1997). Folding dynamics of the src SH3 domain. Biochemistry 36, 15685-92.

Doyle R, Simons K, Qian H, Baker D (1997). Local interactions and the optimization of protein folding. Proteins 29, 282-91.

Bystroff C, Baker D (1997). Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins Suppl 1, 167-71.

Scalley ML, Baker D (1997). Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proc. Natl. Acad. Sci. U.S.A. 94, 10636-40.

Simons KT, Kooperberg C, Huang E, Baker D (1997). Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268, 209-25.

Yi Q, Scalley ML, Simons KT, Gladwin ST, Baker D (1997). Characterization of the free energy spectrum of peptostreptococcal protein L. 2, 271-80.

Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D (1997). Functional rapidly folding proteins from simplified amino acid sequences. Nat. Struct. Biol. 4, 805-9.

Han KF, Baker D (1996). Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc. Natl. Acad. Sci. U.S.A. 93, 5814-8.

Yi Q, Baker D (1996). Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein Sci. 5, 1060-6.

Bystroff C, Simons KT, Han KF, Baker D (1996). Local sequence-structure correlations in proteins. Curr. Opin. Biotechnol. 7, 417-21.

Han KF, Baker D (1995). Recurring local sequence motifs in proteins. J. Mol. Biol. 251, 176-87.[Full Text PDF]

Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, Baker D (1995). A phage display system for studying the sequence determinants of protein folding. Protein Sci. 4, 1108-17.

Last updated Mon Nov 9 13:08:15 2009