Literature DB >> 12163064

Rotamer libraries in the 21st century.

Roland L Dunbrack1.   

Abstract

Rotamer libraries are widely used in protein structure prediction, protein design, and structure refinement. As the size of the structure data base has increased rapidly in recent years, it has become possible to derive well-refined rotamer libraries using strict criteria for data inclusion and for studying dependence of rotamer populations and dihedral angles on local structural features.

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Year:  2002        PMID: 12163064     DOI: 10.1016/s0959-440x(02)00344-5

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  239 in total

1.  SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations.

Authors:  Ken Nagata; Arlo Randall; Pierre Baldi
Journal:  Proteins       Date:  2011-11-09

2.  Protein-protein docking with a reduced protein model accounting for side-chain flexibility.

Authors:  Martin Zacharias
Journal:  Protein Sci       Date:  2003-06       Impact factor: 6.725

3.  Analysis of forces that determine helix formation in alpha-proteins.

Authors:  Gelena T Kilosanidze; Alexey S Kutsenko; Natalia G Esipova; Vladimir G Tumanyan
Journal:  Protein Sci       Date:  2004-02       Impact factor: 6.725

Review 4.  Structural genomics: computational methods for structure analysis.

Authors:  Sharon Goldsmith-Fischman; Barry Honig
Journal:  Protein Sci       Date:  2003-09       Impact factor: 6.725

5.  A graph-theory algorithm for rapid protein side-chain prediction.

Authors:  Adrian A Canutescu; Andrew A Shelenkov; Roland L Dunbrack
Journal:  Protein Sci       Date:  2003-09       Impact factor: 6.725

6.  Anchor residues in protein-protein interactions.

Authors:  Deepa Rajamani; Spencer Thiel; Sandor Vajda; Carlos J Camacho
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-21       Impact factor: 11.205

7.  Analysis of side-chain rotamers in transmembrane proteins.

Authors:  Aaron K Chamberlain; James U Bowie
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

8.  Optimization of van der Waals energy for protein side-chain placement and design.

Authors:  Amr Fahmy; Gerhard Wagner
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

9.  Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20.

Authors:  Dustin M McCraw; Jason K O'Donnell; Kenneth A Taylor; Scott M Stagg; Michael S Chapman
Journal:  Virology       Date:  2012-06-09       Impact factor: 3.616

10.  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.

Authors:  Oliver F Lange; Paolo Rossi; Nikolaos G Sgourakis; Yifan Song; Hsiau-Wei Lee; James M Aramini; Asli Ertekin; Rong Xiao; Thomas B Acton; Gaetano T Montelione; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-25       Impact factor: 11.205

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