Research Topics
Genomes and Genes | David BakerSummaryAffiliation: University of Washington Country: USA Publications
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Publications
Ab initio protein structure prediction: progress and prospectsR Bonneau
Department of Biochemistry, University of Washington, Seattle, Washington, Box 357350, 98195, USA
Annu Rev Biophys Biomol Struct 30:173-89. 2001..In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work...- Protein structure prediction and structural genomicsD Baker
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Science 294:93-6. 2001..We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics... - Prediction and design of macromolecular structures and interactionsDavid Baker
University of Washington, Seattle, WA 98112, USA
Philos Trans R Soc Lond B Biol Sci 361:459-63. 2006..I emphasize the results from the prediction and design tests that suggest progress is being made in high-resolution modelling, and that there is hope for reliably and accurately computing structural biology... - Free modeling with Rosetta in CASP6Philip Bradley
University of Washington, Seattle, Washington 98195, USA
Proteins 61:128-34. 2005..Highlights include improved performance on larger proteins (100-200 residues) and the prediction of a 70-residue alpha-beta protein to near-atomic resolution... - Design of a novel globular protein fold with atomic-level accuracyBrian Kuhlman
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 302:1364-8. 2003..2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature... - A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfacesLin Jiang
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 58:893-904. 2005.... - Prediction of CASP6 structures using automated Robetta protocolsDylan Chivian
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 61:157-66. 2005..The most significant finding from CASP5, that automated protocols can be roughly comparable in ability with the better human-intervention predictors, is repeated here in CASP6... - Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reactionJustin B Siegel
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 329:309-13. 2010..Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry... - RosettaDock in CAPRI rounds 6-12Chu Wang
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 69:758-63. 2007..Motivated by these CAPRI challenges, we have made progress in reformulating RosettaDock using a "fold-tree" representation, which provides a general framework for treating a wide variety of flexible-backbone docking problems... - Kemp elimination catalysts by computational enzyme designDaniela Röthlisberger
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 453:190-5. 2008..These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future... - Computational thermostabilization of an enzymeAaron Korkegian
Division of Basic Sciences, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA
Science 308:857-60. 2005..The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering... - Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOMDavid E Kim
University of Washington, Seattle, Washington 98195, USA
Proteins 61:193-200. 2005..We describe here the successes and failures using both methods, and address the possibility of incorporating both protocols into an improved hybrid method... - Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolutionGautam Dantas
Department of Biochemistry, University of Washington, Seattle 98195, USA
J Mol Biol 362:1004-24. 2006..The symmetric self-association between two identical mis-translated CFr sub-domains to generate an extremely stable structure parallels a mechanism for natural protein-fold evolution by modular recombination of protein sub-structures... - A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoformsMichael R Sawaya
Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, Los Angeles, CA 90095, USA
Cell 134:1007-18. 2008..These studies provide insight into how "matching" at all three pairs of variable domains in Dscam mediates isoform-specific recognition... - A new twist in TCR diversity revealed by a forbidden alphabeta TCRChristine McBeth
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
J Mol Biol 375:1306-19. 2008.... - Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibilityOra Schueler-Furman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 60:187-94. 2005.... - High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein designGautam Dantas
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 366:1209-21. 2007.... - High-resolution structure prediction and the crystallographic phase problemBin Qian
University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Box 357350, Seattle 98195, USA
Nature 450:259-64. 2007.... - A putative Src homology 3 domain binding motif but not the C-terminal dystrophin WW domain binding motif is required for dystroglycan function in cellular polarity in DrosophilaAndriy S Yatsenko
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
J Biol Chem 282:15159-69. 2007..This suggests that an SH3-containing protein, which has yet to be identified, functionally interacts with Dg... - Rosetta predictions in CASP5: successes, failures, and prospects for complete automationPhilip Bradley
Department of Biochemistry, University of Washington, Seattle 98195-7350, USA
Proteins 53:457-68. 2003..For the three targets where the human-assisted predictions were significantly closer to the native structure, we identify the steps that remain to be automated... - Computational redesign of endonuclease DNA binding and cleavage specificityJustin Ashworth
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 441:656-9. 2006..These results suggest that computational protein design methods can have an important role in the creation of novel highly specific endonucleases for gene therapy and other applications... - Exploitation of binding energy for catalysis and designSummer B Thyme
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 461:1300-4. 2009..Our results illustrate how classical enzymology and modern protein design can each inform the other... - Automated prediction of CASP-5 structures using the Robetta serverDylan Chivian
University of Washington, Seattle 98195, USA
Proteins 53:524-33. 2003..The Robetta server produced quite reasonable predictions for targets in the recent CASP-5 and CAFASP-3 experiments, some of which were at the level of the best human predictions... - Structure prediction for CASP8 with all-atom refinement using RosettaSrivatsan Raman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 77:89-99. 2009..These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy... - Computation-guided backbone grafting of a discontinuous motif onto a protein scaffoldMihai L Azoitei
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 334:373-6. 2011..The method can be generalized to design other functional proteins through backbone grafting... - De novo computational design of retro-aldol enzymesLin Jiang
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 319:1387-91. 2008..The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model... - Computational design of proteins targeting the conserved stem region of influenza hemagglutininSarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 332:816-21. 2011..Such designed binding proteins may be useful for both diagnostics and therapeutics... - The highly cooperative folding of small naturally occurring proteins is likely the result of natural selectionAlexander L Watters
Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
Cell 128:613-24. 2007.... - Toward high-resolution de novo structure prediction for small proteinsPhilip Bradley
University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA
Science 309:1868-71. 2005..5 angstroms) can be achieved for small protein domains (<85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling... - Computation of conformational coupling in allosteric proteinsBrian A Kidd
Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
PLoS Comput Biol 5:e1000484. 2009.... - New algorithms and an in silico benchmark for computational enzyme designAlexandre Zanghellini
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Protein Sci 15:2785-94. 2006..The new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design... - Macromolecular modeling with rosettaRhiju Das
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Annu Rev Biochem 77:363-82. 2008..Emerging connections to crystallographic phasing, NMR modeling, and lower-resolution approaches are described and critically assessed... - Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interfaceLukasz A Joachimiak
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, 98195-7350, USA
J Mol Biol 361:195-208. 2006..This multi-step approach should be applicable to the design of polar protein-protein interactions and contribute to the re-engineering of regulatory networks mediated by protein-protein interactions... - Rosetta in CAPRI rounds 13-19Sarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 78:3212-8. 2010..Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement... - Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formationStuart A Sievers
Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Box 951970, Los Angeles, California 90095 1570, USA
Nature 475:96-100. 2011..Because the inhibiting peptides have been designed on structures of dual-?-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers... - Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformationsJeffrey J Gray
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, J-567 Health Sciences, Box 357350, Seattle, WA 98195, USA
J Mol Biol 331:281-99. 2003.... - A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteinsGautam Dantas
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 332:449-60. 2003..These encouraging results indicate that the computational protein design methods can, with significant reliability, identify amino acid sequences compatible with a target protein backbone... - Predicting protein structures with a multiplayer online gameSeth Cooper
Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA
Nature 466:756-60. 2010.... - Contact order and ab initio protein structure predictionRichard Bonneau
Department of Biochemistry, University of Washington, Seattle 98195, USA
Protein Sci 11:1937-44. 2002.... - Algorithm discovery by protein folding game playersFiras Khatib
Department of Biochemistry, University of Washington, Box 357370, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 108:18949-53. 2011..Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms... - RosettaRemodel: a generalized framework for flexible backbone protein designPo Ssu Huang
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
PLoS ONE 6:e24109. 2011.... - RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suiteSarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
PLoS ONE 6:e20161. 2011.... - NMR structure determination for larger proteins using backbone-only dataSrivatsan Raman
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 327:1014-8. 2010..The new method is not hindered by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kilodaltons and should enable routine NMR structure determination for larger proteins... - Hotspot-centric de novo design of protein bindersSarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 413:1047-62. 2011..We show that the method generates binding surfaces that are more conformationally restricted than previous design methods, reducing opportunities for off-target interactions... - RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validationWill Sheffler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
Protein Sci 18:229-39. 2009.... - Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinityCandice S E Lengyel
Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, Washington 98119, USA
J Biol Chem 282:30658-66. 2007..Five of these had affinities enhanced by 0.9-1.8 kcal/mol over wild type by one to three non-contacting substitutions. Therefore, in this case, mutations designed to mildly destabilize a protein enhanced association and affinity... - Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linkingAlex Zelter
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
J Proteome Res 9:3583-9. 2010..The remaining 3 cross-links are likely due to protein aggregation. The accuracy and rapid throughput of our workflow will advance the use of protein cross-linking in structural biology... - A de novo protein binding pair by computational design and directed evolutionJohn Karanicolas
Department of Biochemistry, University of Washington, Seattle, WA 98195 7350, USA
Mol Cell 42:250-60. 2011..This work demonstrates that high-affinity protein interfaces can be created by designing complementary interaction surfaces on two noninteracting partners and underscores remaining challenges... - Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairsJustin Ashworth
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Nucleic Acids Res 38:5601-8. 2010.... - Protein structure prediction and analysis using the Robetta serverDavid E Kim
Structural Genomics of Pathogenic Protozoa, Department of Biochemistry, University of Washington, Seattle WA 98195, USA
Nucleic Acids Res 32:W526-31. 2004..The Rosetta protein design and protein-protein docking methodologies will soon be available through the server as well... - Alternate states of proteins revealed by detailed energy landscape mappingMichael D Tyka
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 405:607-18. 2011.... - Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontologyLars Malmström
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
PLoS Biol 5:e76. 2007..The domain predictions and structural information are available in an online database at http://rd.plos.org/10.1371_journal.pbio.0050076_01... - On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymesHyundae D Cho
Department of Biochemistry, School of Medicine, University of Washington, Seattle, Washington 98195 7350, USA
RNA 14:1284-9. 2008..Rather, the data are consistent with a transient conformational change involving P295 of the tRNA-binding alpha-helix during or between one or more steps in CCA addition... - Structure similarity measure with penalty for close non-equivalent residuesRuslan I Sadreyev
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
Bioinformatics 25:1259-63. 2009.... - Motif-directed flexible backbone design of functional interactionsJames J Havranek
Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Protein Sci 18:1293-305. 2009..We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations... - De novo prediction of three-dimensional structures for major protein familiesRichard Bonneau
Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
J Mol Biol 322:65-78. 2002.... - Protein-protein docking with backbone flexibilityChu Wang
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
J Mol Biol 373:503-19. 2007..The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models... - Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@homeRhiju Das
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 69:118-28. 2007..These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions... - A simple physical model for the prediction and design of protein-DNA interactionsJames J Havranek
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 344:59-70. 2004..When combined with algorithms that optimize specificity directly, the simple computational model developed here should be useful for the engineering of proteins with novel DNA-binding specificities... - Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational designGong Cheng
Department of Biochemistry, University of Washington Seattle, Washington, USA
Nucleic Acids Res 33:5861-7. 2005..The combined sequence and structure based functional site prediction method has been implemented in a publicly available web server... - A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoysYu Chen
Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
Nucleic Acids Res 32:5147-62. 2004..By incorporating the new hydrogen-bonding potential into a physical model of protein-RNA interfaces with full atom representation, we were able to recover native amino acids at protein-RNA interfaces... - Modeling symmetric macromolecular structures in Rosetta3Frank DiMaio
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
PLoS ONE 6:e20450. 2011..Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems... - Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme designLing Wang
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 415:615-25. 2012..The covalently bound complex structures and mutagenesis data highlight the strengths and weaknesses of the de novo enzyme design strategy... - Computational redesign of protein-protein interaction specificityTanja Kortemme
Howard Hughes Medical Institute and Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195-7350, USA
Nat Struct Mol Biol 11:371-9. 2004..The approach should be applicable to the design of interacting protein pairs with novel specificities for delineating and re-engineering protein interaction networks in living cells... - Design, activity, and structure of a highly specific artificial endonucleaseBrett S Chevalier
Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue N. A3-023, Seattle, WA 98109, USA
Mol Cell 10:895-905. 2002..These results indicate that it may be possible to generate novel highly specific DNA binding proteins from homing endonucleases... - Accurate computer-based design of a new backbone conformation in the second turn of protein LBrian Kuhlman
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 315:471-7. 2002..2 A). The folding rates of the redesigned proteins are greater than that of the wild-type protein and in contrast to wild-type protein L the second beta-turn appears to be formed at the rate limiting step in folding... - Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formationR Bonneau
Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington, USA
Proteins 43:1-11. 2001..Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set. Proteins 2001;43:1-11... - Automated de novo prediction of native-like RNA tertiary structuresRhiju Das
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Box 357350, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 104:14664-9. 2007.... - Protein-protein docking predictions for the CAPRI experimentJeffrey J Gray
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington, USA
Proteins 52:118-22. 2003..Using a preliminary version of the protocol in round 1, target 1 was predicted within 8.8 A although few contacts were correct. For targets 2 and 3, the interface locations and a small fraction of the contacts were correctly identified... - Computer-based redesign of a protein folding pathwayS Nauli
1] Department of Biochemistry and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA
Nat Struct Biol 8:602-5. 2001..Kinetic studies show that the redesigned proteins fold approximately 100 x faster than wild type protein and that the first beta-turn is formed and the second disrupted at the rate limiting step in folding... - Functional inferences from blind ab initio protein structure predictionsR Bonneau
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
J Struct Biol 134:186-90. 2001.... - Prospects for de novo phasing with de novo protein modelsRhiju Das
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Acta Crystallogr D Biol Crystallogr 65:169-75. 2009..Improvements in conformational search methods will be necessary if molecular replacement with de novo models is to become a practical tool for targets without homology to previously solved protein structures... - High-resolution structural validation of the computational redesign of human U1A proteinNeil Dobson
Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
Structure 14:847-56. 2006..The dynamics of the backbone of the redesigned protein also mirror those of human U1A, suggesting that the protein design algorithm captures the shape of the potential energy landscape in addition to the local energy minimum... - Computational alanine scanning of protein-protein interfacesTanja Kortemme
Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California San Francisco, CA 94107, USA
Sci STKE 2004:pl2. 2004.... - RosettaLigand docking with full ligand and receptor flexibilityIan W Davis
Department of Biochemistry, University of Washington, Seattle, WA 98195 7350, USA
J Mol Biol 385:381-92. 2009..On a challenging set of retrospective and prospective cross-docking tests, we find that the top-scoring ligand pose is correctly positioned within 2 A RMSD for 64% (54/85) of cases overall... - Ab initio methodsDylan Chivian
Department of Biochemistry, University of Washington, Seattle, WA, USA
Methods Biochem Anal 44:547-57. 2003 - Maternal toxicity with continuous nevirapine in pregnancy: results from PACTG 1022Jane Hitti
University of Washington, Seattle, 98195, USA
J Acquir Immune Defic Syndr 36:772-6. 2004..To compare the safety of nelfinavir and nevirapine-based antiretroviral treatment in HIV-1-infected pregnant women... - Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2Sehat Nauli
Department of Biochemistry, University of Washington, Seattle 98195, USA
Protein Sci 11:2924-31. 2002..A second round of structure-based design yielded new variants of NuG1 and NuG2, which are further stabilized by 0.5 kcal/mole and 0.9 kcal/mole... - The utility of early end-tidal capnography in monitoring ventilation status after severe injuryKeir J Warner
Department of Trauma Surgery, Harborview Medical Center, Seattle, Washington 98104, USA
J Trauma 66:26-31. 2009..Thus, we hypothesize that EtCO2 will demonstrate a poor reflection of actual ventilation status after severe injury... - Sampling bottlenecks in de novo protein structure predictionDavid E Kim
Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
J Mol Biol 393:249-60. 2009..In a number of proteins, the linchpin features are in regions found experimentally to form late in folding, suggesting a correspondence between folding in silico and in reality... - Refinement of protein structures into low-resolution density maps using rosettaFrank DiMaio
Department of Biochemistry, University of Washington, Seattle, 98195, USA
J Mol Biol 392:181-90. 2009..The method can achieve near-atomic resolution starting from density maps at 4-6 A resolution... - Recapitulation and design of protein binding peptide structures and sequencesVanita D Sood
Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195, USA
J Mol Biol 357:917-27. 2006..Based on these in silico and experimental results, we discuss future applications of the approach to the prediction and design of protein-peptide interactions... - Assessment of the optimization of affinity and specificity at protein-DNA interfacesJustin Ashworth
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Nucleic Acids Res 37:e73. 2009..The approach provides a complement to traditional methods of mutational analysis, and should be useful for rapidly formulating hypotheses about the roles of amino acid residues in protein-DNA interfaces... - De novo enzyme design using Rosetta3Florian Richter
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
PLoS ONE 6:e19230. 2011..Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction... - Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggednessMaximilian Schlosshauer
Department of Physics, University of Washington, Seattle, WA 98195, USA
Protein Sci 13:1660-9. 2004..The transparent physical interpretation of our approach that computes association rates directly from the size and geometry of protein-protein binding funnels makes it a useful complement to Brownian dynamics simulations... - Simplified proteins: minimalist solutions to the 'protein folding problem'K W Plaxco
Department of Biochemistry, University of Washington, Seattle 98195, USA
Curr Opin Struct Biol 8:80-5. 1998..They may also have important implications for protein design and for theories of the origins of protein synthesis itself... - Local sequence-structure correlations in proteinsC Bystroff
Department of Biochemistry, University of Washington, Seattle 98195, USA
Curr Opin Biotechnol 7:417-21. 1996..Recent highlights include numerous studies of the structures adopted by short peptides, new approaches to correlating sequence patterns with structure patterns, and folding simulations using simple potentials... - Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitutionD E Kim
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
Acta Crystallogr D Biol Crystallogr 57:480-7. 2001..These high-resolution structures of the tryptophan-containing variant provide a reference frame for the analysis of thermodynamic and kinetic data derived from a series of mutational studies of the protein L B1 domain... - Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnusD E Kim
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
Structure 9:1017-27. 2001..One is the strain in the second beta turn that favors the dimer, and the other is the entropic cost of dimer formation that favors the monomer. A single-site mutation can disrupt this balance and trigger domain swapping... - Prospects for ab initio protein structural genomicsK T Simons
Unversity of Washington, Seattle, WA 98195, USA
J Mol Biol 306:1191-9. 2001.... - Evolutionary conservation in protein folding kineticsK W Plaxco
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
J Mol Biol 298:303-12. 2000..Thus the structure of the folding transition state ensemble appears to be more highly conserved than the specific interactions that stabilize it... - Prediction of local structure in proteins using a library of sequence-structure motifsC Bystroff
Department of Biochemistry, University of Washington, Seattle, WA, 98195 7350, USA
J Mol Biol 281:565-77. 1998..The predictions are complementary to traditional secondary structure predictions because they are considerably more specific in turn regions, and may contribute to ab initio tertiary structure prediction and fold recognition... - Emergence of symmetry in homooligomeric biological assembliesIngemar Andre
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 105:16148-52. 2008..02% in the overall population to >50% in very low energy subpopulations... - Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selectionMichelle Scalley-Kim
Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
J Mol Biol 338:573-83. 2004.... - Alteration of enzyme specificity by computational loop remodeling and designPaul M Murphy
Department of Biochemistry, Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 106:9215-20. 2009..5e6-fold. The structure of the designed protein was confirmed by X-ray crystallographic analysis: The remodeled loop adopts a conformation that is within 1-A Calpha RMSD of the computational model... - Deciphering a novel thioredoxin-like fold familyLisa N Kinch
Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA
Proteins 52:323-31. 2003..Finally, the rosetta-derived model structure assists us in assembling a global multiple-sequence alignment of COG3019 with two other thioredoxin-like fold families, the thioltransferases and the bacterial arsenate reductases (ArsC)... - Blind docking of pharmaceutically relevant compounds using RosettaLigandIan W Davis
Department of Biochemistry, University of Washington, Seattle, Washington 98195 7350, USA
Protein Sci 18:1998-2002. 2009.... - Rosetta in CASP4: progress in ab initio protein structure predictionR Bonneau
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins . 2001..These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information... - Toward high-resolution prediction and design of transmembrane helical protein structuresP Barth
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 104:15682-7. 2007.... - Circularization changes the folding transition state of the src SH3 domainV P Grantcharova
Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
J Mol Biol 306:555-63. 2001.... - A "loop entropy reduction" phage-display selection for folded amino acid sequencesP Minard
Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
Protein Sci 10:129-34. 2001..The results indicate that the loop entropy reduction screen is capable of discriminating folded from unfolded sequences when the proper host protein and insertion point are chosen...
Research Grants
- High resolution structure modeling with RosettaDavid Baker; Fiscal Year: 2010..Such structures could provide insight into fundamental biological processes and the basis for disease causing mutations, and allow the structure based design of new therapeutics. ..
- FOLDING AND DESIGN OF ALPHA BETA SANDWICH PROTEINSDavid Baker; Fiscal Year: 2003..abstract_text> ..
- MECHANISM OF FOLDING OF THE SH3 DOMAINDavid Baker; Fiscal Year: 2002..abstract_text> ..
- Protein-Protein InteractionsDavid Baker; Fiscal Year: 2009....