Literature DB >> 12827678

On the kinematics of protein folding.

Sean Cahill1, Michael Cahill, Kevin Cahill.   

Abstract

We offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that closes it. Copyright 2003 Wiley Periodicals, Inc.

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Year:  2003        PMID： 12827678     DOI： 10.1002/jcc.10245

Source DB:  PubMed          Journal:  J Comput Chem        ISSN： 0192-8651            Impact factor:   3.376


  12 in total

1.  LMProt: an efficient algorithm for Monte Carlo sampling of protein conformational space.

Authors:  Roosevelt Alves da Silva; Léo Degrève; Antonio Caliri
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

Review 2.  Constraint methods that accelerate free-energy simulations of biomolecules.

Authors:  Alberto Perez; Justin L MacCallum; Evangelos A Coutsias; Ken A Dill
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

3.  Assessing protein loop flexibility by hierarchical Monte Carlo sampling.

Authors:  Jerome Nilmeier; Lan Hua; Evangelos A Coutsias; Matthew P Jacobson
Journal:  J Chem Theory Comput       Date:  2011-05-10       Impact factor: 6.006

4.  Methods for Monte Carlo simulations of biomacromolecules.

Authors:  Andreas Vitalis; Rohit V Pappu
Journal:  Annu Rep Comput Chem       Date:  2009-01-01

Review 5.  Computational models of protein kinematics and dynamics: beyond simulation.

Authors:  Bryant Gipson; David Hsu; Lydia E Kavraki; Jean-Claude Latombe
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2012-04-09       Impact factor: 10.745

6.  Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.

Authors:  Chen Yanover; Philip Bradley
Journal:  Nucleic Acids Res       Date:  2011-02-22       Impact factor: 16.971

7.  Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

Authors:  Trevor W Siggers; Barry Honig
Journal:  Nucleic Acids Res       Date:  2007-01-30       Impact factor: 16.971

Review 8.  Conformational sampling in template-free protein loop structure modeling: an overview.

Authors:  Yaohang Li
Journal:  Comput Struct Biotechnol J       Date:  2013-02-25       Impact factor: 7.271

9.  A self-organizing algorithm for modeling protein loops.

Authors:  Pu Liu; Fangqiang Zhu; Dmitrii N Rassokhin; Dimitris K Agrafiotis
Journal:  PLoS Comput Biol       Date:  2009-08-21       Impact factor: 4.475

10.  Loop modeling: Sampling, filtering, and scoring.

Authors:  Cinque S Soto; Marc Fasnacht; Jiang Zhu; Lucy Forrest; Barry Honig
Journal:  Proteins       Date:  2008-02-15
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