Literature DB >> 18215513

Computational techniques for efficient conformational sampling of proteins.

Adam Liwo1, Cezary Czaplewski, Stanisław Ołdziej, Harold A Scheraga.   

Abstract

In this review, we summarize the computational methods for sampling the conformational space of biomacromolecules. We discuss the methods applicable to find only lowest energy conformations (global minimization of the potential-energy function) and to generate canonical ensembles (canonical Monte Carlo method and canonical molecular dynamics method and their extensions). Special attention is devoted to the use of coarse-grained models that enable simulations to be enhanced by several orders of magnitude.

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Year:  2008        PMID： 18215513      PMCID： PMC2465814          DOI： 10.1016/j.sbi.2007.12.001

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


  32 in total

1.  Generation of accurate protein loop conformations through low-barrier molecular dynamics.

Authors:  Viktor Hornak; Carlos Simmerling
Journal:  Proteins       Date:  2003-06-01

2.  Multiplexed-replica exchange molecular dynamics method for protein folding simulation.

Authors:  Young Min Rhee; Vijay S Pande
Journal:  Biophys J       Date:  2003-02       Impact factor: 4.033

3.  Intermediates and the folding of proteins L and G.

Authors:  Scott Brown; Teresa Head-Gordon
Journal:  Protein Sci       Date:  2004-04       Impact factor: 6.725

4.  Optimized parallel tempering simulations of proteins.

Authors:  Simon Trebst; Matthias Troyer; Ulrich H E Hansmann
Journal:  J Chem Phys       Date:  2006-05-07       Impact factor: 3.488

5.  Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations.

Authors:  Jakob P Ulmschneider; Martin B Ulmschneider; Alfredo Di Nola
Journal:  J Phys Chem B       Date:  2006-08-24       Impact factor: 2.991

6.  Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

Authors:  Pu Liu; Xuhui Huang; Ruhong Zhou; B J Berne
Journal:  J Phys Chem B       Date:  2006-09-28       Impact factor: 2.991

7.  Folding pathway of the b1 domain of protein G explored by multiscale modeling.

Authors:  Sebastian Kmiecik; Andrzej Kolinski
Journal:  Biophys J       Date:  2007-09-21       Impact factor: 4.033

8.  Self-consistently optimized energy functions for protein structure prediction by molecular dynamics.

Authors:  K K Koretke; Z Luthey-Schulten; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1998-03-17       Impact factor: 11.205

9.  MONSSTER: a method for folding globular proteins with a small number of distance restraints.

Authors:  J Skolnick; A Kolinski; A R Ortiz
Journal:  J Mol Biol       Date:  1997-01-17       Impact factor: 5.469

10.  Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Authors:  S Ołdziej; C Czaplewski; A Liwo; M Chinchio; M Nanias; J A Vila; M Khalili; Y A Arnautova; A Jagielska; M Makowski; H D Schafroth; R Kaźmierkiewicz; D R Ripoll; J Pillardy; J A Saunders; Y K Kang; K D Gibson; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-13       Impact factor: 11.205
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  43 in total

Review 1.  Computational methods in drug discovery.

Authors:  Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal:  Pharmacol Rev       Date:  2013-12-31       Impact factor: 25.468

Review 2.  Biomolecularmodeling and simulation: a field coming of age.

Authors:  Tamar Schlick; Rosana Collepardo-Guevara; Leif Arthur Halvorsen; Segun Jung; Xia Xiao
Journal:  Q Rev Biophys       Date:  2011-05       Impact factor: 5.318

Review 3.  Enhanced sampling techniques in molecular dynamics simulations of biological systems.

Authors:  Rafael C Bernardi; Marcelo C R Melo; Klaus Schulten
Journal:  Biochim Biophys Acta       Date:  2014-10-23

4.  Emerging topics in structure-based virtual screening.

Authors:  Giulio Rastelli
Journal:  Pharm Res       Date:  2013-03-07       Impact factor: 4.200

5.  Effect of using suboptimal alignments in template-based protein structure prediction.

Authors:  Hao Chen; Daisuke Kihara
Journal:  Proteins       Date:  2011-01

6.  Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding.

Authors:  Jinan Wang; Yinglong Miao
Journal:  J Chem Phys       Date:  2020-10-21       Impact factor: 3.488

7.  Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure.

Authors:  Tamar Schlick
Journal:  F1000 Biol Rep       Date:  2009-06-29

8.  T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges.

Authors:  Matthew N Davies; Darren R Flower; Kanchan Phadwal; Isabel K Macdonald; Peter V Coveney; Shunzhou Wan
Journal:  Immunome Res       Date:  2010-11-03

9.  Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

Authors:  Yinglong Miao; J Andrew McCammon
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

10.  Studies of alpha-helicity and intersegmental interactions in voltage-gated Na+ channels: S2D4.

Authors:  Zhongming Ma; Jun Kong; Roland G Kallen
Journal:  PLoS One       Date:  2009-11-02       Impact factor: 3.240
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