Literature DB >> 8728655

Mean-field minimization methods for biological macromolecules.

P Koehl1, M Delarue.   

Abstract

Simulations of macromolecular structures involve the minimization of a potential-energy function that presents many local minima. Mean-field theory provides a tool that enables us to escape these minima, by enhancing sampling in conformational space. The number of applications of this technique has increased significantly over the past year, enabling problems with protein-homology modelling and inverted protein structure prediction to be solved.

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Year:  1996        PMID: 8728655     DOI: 10.1016/s0959-440x(96)80078-9

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


  22 in total

1.  Computational method to reduce the search space for directed protein evolution.

Authors:  C A Voigt; S L Mayo; F H Arnold; Z G Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2001-03-27       Impact factor: 11.205

2.  Meanfield approach to the thermodynamics of protein-solvent systems with application to p53.

Authors:  A R Völkel; J Noolandi
Journal:  Biophys J       Date:  2001-03       Impact factor: 4.033

3.  Optimization of nucleic acid sequences.

Authors:  I Lafontaine; R Lavery
Journal:  Biophys J       Date:  2000-08       Impact factor: 4.033

4.  Improved recognition of native-like protein structures using a family of designed sequences.

Authors:  Patrice Koehl; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-08       Impact factor: 11.205

5.  Enhanced sampling of the molecular potential energy surface using mutually orthogonal latin squares: application to peptide structures.

Authors:  K Vengadesan; N Gautham
Journal:  Biophys J       Date:  2003-05       Impact factor: 4.033

6.  All are not equal: a benchmark of different homology modeling programs.

Authors:  Björn Wallner; Arne Elofsson
Journal:  Protein Sci       Date:  2005-05       Impact factor: 6.725

Review 7.  Advances in homology protein structure modeling.

Authors:  Zhexin Xiang
Journal:  Curr Protein Pept Sci       Date:  2006-06       Impact factor: 3.272

Review 8.  Exploring conformational space using a mean field technique with MOLS sampling.

Authors:  P Arun Prasad; V Kanagasabai; J Arunachalam; N Gautham
Journal:  J Biosci       Date:  2007-08       Impact factor: 1.826

9.  IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.

Authors:  Christoph Hartmann; Iris Antes; Thomas Lengauer
Journal:  Protein Sci       Date:  2007-06-13       Impact factor: 6.725

10.  Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities.

Authors:  Peng Zhou; Xiang Chen; Zhicai Shang
Journal:  J Comput Aided Mol Des       Date:  2008-10-08       Impact factor: 3.686

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