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Pubs
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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 -
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 -
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 -
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 -
Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L (2004)
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.
Genome Biol 5:R52 -
Malmström J, Larsen K, Malmström L, Tufvesson E, Parker K, Marchese J, Williamson B, Hattan S, Patterson D, Martin S, Graber A, Juhasz HP, Westergren-Thorsson G, Marko-Varga G (2004)
Proteome annotations and identifications of the human pulmonary fibroblast.
J Proteome Res 3:525-37 -
Kim DE, Chivian D, Baker D (2004)
Protein structure prediction and analysis using the Robetta server.
Nucleic Acids Res 32:W526-31 -
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 -
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 -
Kuhlman B, Baker D (2004)
Exploring folding free energy landscapes using computational protein design.
Curr Opin Struct Biol 14:89-95