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David Kim

Research Profile

Physiology

Concepts & Ideas

Living Beings

Peptostreptococcus

Chemicals & Drugs

Occupations

Activities & Behaviors

Procedures

Sequence Alignment

Disorders

Protein Denaturation

Co-author Network

Publications

TOP 3
David E Kim; Ben Blum; Philip Bradley; David Baker
Sampling bottlenecks in de novo protein structure prediction.
Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D Tyka; Divya Bhat; Dylan Chivian; David E Kim; William H Sheffler; Lars Malmström; Andrew M Wollacott; Chu Wang; Ingemar Andre; David Baker
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Kira M S Misura; Dylan Chivian; Carol A Rohl; David E Kim; David Baker
Physically realistic homology models built with ROSETTA can be more accurate than their templates.

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All Publications

2009: David E Kim; Ben Blum; Philip Bradley; David Baker
Sampling bottlenecks in de novo protein structure prediction.
Journal of molecular biology 2009;393(1):249-60.
2007: Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D Tyka; Divya Bhat; Dylan Chivian; David E Kim; William H Sheffler; Lars Malmström; Andrew M Wollacott; Chu Wang; Ingemar Andre; David Baker
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Proteins 2007;69 Suppl 8():118-28.
2006: Kira M S Misura; Dylan Chivian; Carol A Rohl; David E Kim; David Baker
Physically realistic homology models built with ROSETTA can be more accurate than their templates.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(14):5361-6.
2005: David E Kim; Dylan Chivian; Lars Malmström; David Baker
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.
Proteins 2005;61 Suppl 7():193-200.
2005: Dylan Chivian; David E Kim; Lars Malmström; Jack Schonbrun; Carol A Rohl; David Baker
Prediction of CASP6 structures using automated Robetta protocols.
Proteins 2005;61 Suppl 7():157-66.
2005: Philip Bradley; Lars Malmström; Bin Qian; Jack Schonbrun; Dylan Chivian; David E Kim; Jens Meiler; Kira M S Misura; David Baker
Free modeling with Rosetta in CASP6.
Proteins 2005;61 Suppl 7():128-34.
2004: David E Kim; Dylan Chivian; David Baker
Protein structure prediction and analysis using the Robetta server.
Nucleic acids research 2004;32(Web Server issue):W526-31.
2003: Dylan Chivian; David E Kim; Lars Malmström; Philip Bradley; Timothy Robertson; Paul Murphy; Charlie E M Strauss; Richard Bonneau; Carol A Rohl; David Baker
Automated prediction of CASP-5 structures using the Robetta server.
Proteins 2003;53 Suppl 6():524-33.
2002: Brian Kuhlman; Jason W O'Neill; David E Kim; Kam Y J Zhang; David Baker
Accurate computer-based design of a new backbone conformation in the second turn of protein L.
Journal of molecular biology 2002;315(3):471-7.
2001: Jason W O'Neill; David E Kim; K Johnsen; David Baker; Kam Y J Zhang
Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus.
Structure (London, England : 1993) 2001;9(11):1017-27.
2001: Brian Kuhlman; Jason W O'Neill; David E Kim; Kam Y J Zhang; David Baker
Conversion of monomeric protein L to an obligate dimer by computational protein design.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10687-91.
2001: Jason W O'Neill; David E Kim; David Baker; Kam Y J Zhang
Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.
Acta crystallographica. Section D, Biological crystallography 2001;57(Pt 4):480-7.
2000: David E Kim; C Fisher; David Baker
A breakdown of symmetry in the folding transition state of protein L.
Journal of molecular biology 2000;298(5):971-84.
2000: K Johnsen; Jason W O'Neill; David E Kim; David Baker; Kam Y J Zhang
Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus.
Acta crystallographica. Section D, Biological crystallography 2000;56(Pt 4):506-8.
1999: H Gu; N Doshi; David E Kim; Kim Simons; JV Santiago; Sehat Nauli; David Baker
Robustness of protein folding kinetics to surface hydrophobic substitutions.
Protein science : a publication of the Protein Society 1999;8(12):2734-41.
1998: David E Kim; Qian Yi; ST Gladwin; J M Goldberg; David Baker
The single helix in protein L is largely disrupted at the rate-limiting step in folding.
Journal of molecular biology 1998;284(3):807-15.
1998: David E Kim; H Gu; David Baker
The sequences of small proteins are not extensively optimized for rapid folding by natural selection.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(9):4982-6.