Literature DB >> 16524834

Prediction and design of macromolecular structures and interactions.

David Baker1.   

Abstract

In this article, I summarize recent work from my group directed towards developing an improved model of intra and intermolecular interactions and applying this improved model to the prediction and design of macromolecular structures and interactions. Prediction and design applications can be of great biological interest in their own right, and also provide very stringent and objective tests which drive the improvement of the model and increases in fundamental understanding. 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.

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Year:  2006        PMID: 16524834      PMCID: PMC1609347          DOI: 10.1098/rstb.2005.1803

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  20 in total

1.  De novo protein structure determination using sparse NMR data.

Authors:  P M Bowers; C E Strauss; D Baker
Journal:  J Biomol NMR       Date:  2000-12       Impact factor: 2.835

2.  Accurate computer-based design of a new backbone conformation in the second turn of protein L.

Authors:  Brian Kuhlman; Jason W O'Neill; David E Kim; Kam Y J Zhang; David Baker
Journal:  J Mol Biol       Date:  2002-01-18       Impact factor: 5.469

3.  De novo determination of protein backbone structure from residual dipolar couplings using Rosetta.

Authors:  Carol A Rohl; David Baker
Journal:  J Am Chem Soc       Date:  2002-03-20       Impact factor: 15.419

4.  Computer-based redesign of a protein folding pathway.

Authors:  S Nauli; B Kuhlman; D Baker
Journal:  Nat Struct Biol       Date:  2001-07

5.  A simple physical model for binding energy hot spots in protein-protein complexes.

Authors:  Tanja Kortemme; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2002-10-15       Impact factor: 11.205

6.  Design, activity, and structure of a highly specific artificial endonuclease.

Authors:  Brett S Chevalier; Tanja Kortemme; Meggen S Chadsey; David Baker; Raymond J Monnat; Barry L Stoddard
Journal:  Mol Cell       Date:  2002-10       Impact factor: 17.970

7.  De novo prediction of three-dimensional structures for major protein families.

Authors:  Richard Bonneau; Charlie E M Strauss; Carol A Rohl; Dylan Chivian; Phillip Bradley; Lars Malmström; Tim Robertson; David Baker
Journal:  J Mol Biol       Date:  2002-09-06       Impact factor: 5.469

8.  Improved side-chain modeling for protein-protein docking.

Authors:  Chu Wang; Ora Schueler-Furman; David Baker
Journal:  Protein Sci       Date:  2005-03-31       Impact factor: 6.725

9.  Prediction of CASP6 structures using automated Robetta protocols.

Authors:  Dylan Chivian; David E Kim; Lars Malmström; Jack Schonbrun; Carol A Rohl; David Baker
Journal:  Proteins       Date:  2005

10.  A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces.

Authors:  Lin Jiang; Brian Kuhlman; Tanja Kortemme; David Baker
Journal:  Proteins       Date:  2005-03-01
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  22 in total

1.  Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction.

Authors:  Tyler J Glembo; S Banu Ozkan
Journal:  Biophys J       Date:  2010-03-17       Impact factor: 4.033

2.  Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

Authors:  Adam Liwo; Mey Khalili; Cezary Czaplewski; Sebastian Kalinowski; Staniłsaw Ołdziej; Katarzyna Wachucik; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2007-01-11       Impact factor: 2.991

Review 3.  Foldamers as versatile frameworks for the design and evolution of function.

Authors:  Catherine M Goodman; Sungwook Choi; Scott Shandler; William F DeGrado
Journal:  Nat Chem Biol       Date:  2007-05       Impact factor: 15.040

4.  Computationally mapping sequence space to understand evolutionary protein engineering.

Authors:  Kathryn A Armstrong; Bruce Tidor
Journal:  Biotechnol Prog       Date:  2007-11-17

5.  Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble.

Authors:  Tong Liu; Steven T Whitten; Vincent J Hilser
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-05       Impact factor: 11.205

6.  Introduction. Bioinformatics: from molecules to systems.

Authors:  David T Jones; Michael J E Sternberg; Janet M Thornton
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-03-29       Impact factor: 6.237

Review 7.  Progress in computational protein design.

Authors:  Shaun M Lippow; Bruce Tidor
Journal:  Curr Opin Biotechnol       Date:  2007-07-20       Impact factor: 9.740

8.  Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.

Authors:  Sebastian Pechmann; Emmanuel D Levy; Gian Gaetano Tartaglia; Michele Vendruscolo
Journal:  Proc Natl Acad Sci U S A       Date:  2009-06-05       Impact factor: 11.205

Review 9.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

10.  Selection and structural analysis of de novo proteins from an alpha3beta3 genetic library.

Authors:  Mariejoy Therese Jumawid; Tsuyoshi Takahashi; Toshimasa Yamazaki; Hiroshi Ashigai; Hisakazu Mihara
Journal:  Protein Sci       Date:  2009-02       Impact factor: 6.725

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