Literature DB >> 20971684

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery.

Freddie R Salsbury1.   

Abstract

Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID： 20971684      PMCID： PMC2981647          DOI： 10.1016/j.coph.2010.09.016

Source DB:  PubMed          Journal:  Curr Opin Pharmacol        ISSN： 1471-4892            Impact factor:   5.547


  46 in total

Review 1.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

2.  A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors:  Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

3.  Generalized Born model with a simple, robust molecular volume correction.

Authors:  John Mongan; Carlos Simmerling; J Andrew McCammon; David A Case; Alexey Onufriev
Journal:  J Chem Theory Comput       Date:  2007-01-01       Impact factor: 6.006

Review 4.  Protein folding simulations: from coarse-grained model to all-atom model.

Authors:  Jian Zhang; Wenfei Li; Jun Wang; Meng Qin; Lei Wu; Zhiqiang Yan; Weixin Xu; Guanghong Zuo; Wei Wang
Journal:  IUBMB Life       Date:  2009-06       Impact factor: 3.885

5.  Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems.

Authors:  Zunnan Huang; Chung F Wong
Journal:  J Phys Chem B       Date:  2009-10-29       Impact factor: 2.991

6.  Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.

Authors:  F R Salsbury; M F Crowley; C L Brooks
Journal:  Proteins       Date:  2001-09-01

7.  Direct binding of Fas-associated death domain (FADD) to the tumor necrosis factor-related apoptosis-inducing ligand receptor DR5 is regulated by the death effector domain of FADD.

Authors:  Lance R Thomas; Adrianna Henson; John C Reed; Freddie R Salsbury; Andrew Thorburn
Journal:  J Biol Chem       Date:  2004-06-01       Impact factor: 5.157

8.  Structure and dynamics of end-to-end loop formation of the penta-peptide Cys-Ala-Gly-Gln-Trp in implicit solvents.

Authors:  In-Chul Yeh; Anders Wallqvist
Journal:  J Phys Chem B       Date:  2009-09-10       Impact factor: 2.991

9.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

Review 10.  Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms.

Authors:  Chung-Jung Tsai; Antonio Del Sol; Ruth Nussinov
Journal:  Mol Biosyst       Date:  2009-01-06
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  36 in total

1.  All-atom MD indicates ion-dependent behavior of therapeutic DNA polymer.

Authors:  Ryan L Melvin; William H Gmeiner; Freddie R Salsbury
Journal:  Phys Chem Chem Phys       Date:  2017-08-23       Impact factor: 3.676

2.  Visualizing correlated motion with HDBSCAN clustering.

Authors:  Ryan L Melvin; Jiajie Xiao; Ryan C Godwin; Kenneth S Berenhaut; Freddie R Salsbury
Journal:  Protein Sci       Date:  2017-09-06       Impact factor: 6.725

3.  Mechanistic insights into thrombin's switch between "slow" and "fast" forms.

Authors:  Jiajie Xiao; Ryan L Melvin; Freddie R Salsbury
Journal:  Phys Chem Chem Phys       Date:  2017-09-20       Impact factor: 3.676

4.  Ensemble properties of network rigidity reveal allosteric mechanisms.

Authors:  Donald J Jacobs; Dennis R Livesay; James M Mottonen; Oleg K Vorov; Andrei Y Istomin; Deeptak Verma
Journal:  Methods Mol Biol       Date:  2012

5.  Insights into protein - DNA interactions, stability and allosteric communications: a computational study of mutSα-DNA recognition complexes.

Authors:  Lacramioara Negureanu; Freddie R Salsbury
Journal:  J Biomol Struct Dyn       Date:  2012

6.  Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.

Authors:  Jiajie Xiao; Ryan L Melvin; Freddie R Salsbury
Journal:  J Biomol Struct Dyn       Date:  2018-03-02

7.  Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin.

Authors:  Jiajie Xiao; Freddie R Salsbury
Journal:  J Biomol Struct Dyn       Date:  2016-11-29

8.  All-atom molecular dynamics comparison of disease-associated zinc fingers.

Authors:  Ryan C Godwin; William H Gmeiner; Freddie R Salsbury
Journal:  J Biomol Struct Dyn       Date:  2017-10-03

9.  Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex.

Authors:  Lacramioara Negureanu; Freddie R Salsbury
Journal:  J Biomol Struct Dyn       Date:  2013-06-25

10.  Visualizing ensembles in structural biology.

Authors:  Ryan L Melvin; Freddie R Salsbury
Journal:  J Mol Graph Model       Date:  2016-05-04       Impact factor: 2.518
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