Literature DB >> 23526422

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles.

Vahid Mirjalili1, Michael Feig.   

Abstract

A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.

Entities:  

Keywords:  force field; model selection; molecular dynamics simulation; scoring; structure prediction

Year:  2012        PMID： 23526422      PMCID： PMC3603382          DOI： 10.1021/ct300962x

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  51 in total

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Authors:  Alexander D MacKerell; Michael Feig; Charles L Brooks
Journal:  J Am Chem Soc       Date:  2004-01-28       Impact factor: 15.419

Review 2.  Protein structure prediction in structure based drug design.

Authors:  Mayuko Takeda-Shitaka; Daisuke Takaya; Chieko Chiba; Hirokazu Tanaka; Hideaki Umeyama
Journal:  Curr Med Chem       Date:  2004-03       Impact factor: 4.530

3.  Exploring the potential of template-based modelling.

Authors:  Braddon K Lance; Charlotte M Deane; Graham R Wood
Journal:  Bioinformatics       Date:  2010-06-04       Impact factor: 6.937

4.  Toward high-resolution de novo structure prediction for small proteins.

Authors:  Philip Bradley; Kira M S Misura; David Baker
Journal:  Science       Date:  2005-09-16       Impact factor: 47.728

Review 5.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

6.  Scoring confidence index: statistical evaluation of ligand binding mode predictions.

Authors:  Maria I Zavodszky; Andrew W Stumpff-Kane; David J Lee; Michael Feig
Journal:  J Comput Aided Mol Des       Date:  2009-01-20       Impact factor: 3.686

7.  Consistent refinement of submitted models at CASP using a knowledge-based potential.

Authors:  Gaurav Chopra; Nir Kalisman; Michael Levitt
Journal:  Proteins       Date:  2010-09

8.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-07-18       Impact factor: 6.006

9.  I-TASSER server for protein 3D structure prediction.

Authors:  Yang Zhang
Journal:  BMC Bioinformatics       Date:  2008-01-23       Impact factor: 3.169

10.  MolProbity: all-atom structure validation for macromolecular crystallography.

Authors:  Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21
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  36 in total

1.  Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.

Authors:  Hugo Guterres; Hui Sun Lee; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2019-10-14       Impact factor: 6.006

2.  Accelerating physical simulations of proteins by leveraging external knowledge.

Authors:  Alberto Perez; Joseph A Morrone; Ken A Dill
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2017-04-19

3.  Probabilistic divergence of a template-based modelling methodology from the ideal protocol.

Authors:  Ashish Runthala
Journal:  J Mol Model       Date:  2021-01-07       Impact factor: 1.810

Review 4.  Molecular Dynamics Simulation for All.

Authors:  Scott A Hollingsworth; Ron O Dror
Journal:  Neuron       Date:  2018-09-19       Impact factor: 17.173

5.  Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.

Authors:  Avishek Kumar; Paul Campitelli; M F Thorpe; S Banu Ozkan
Journal:  Proteins       Date:  2015-11-17

6.  Protein homology model refinement by large-scale energy optimization.

Authors:  Hahnbeom Park; Sergey Ovchinnikov; David E Kim; Frank DiMaio; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2018-03-05       Impact factor: 11.205

7.  PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

Authors:  Lim Heo; Michael Feig
Journal:  Bioinformatics       Date:  2018-03-15       Impact factor: 6.937

8.  Driven to near-experimental accuracy by refinement via molecular dynamics simulations.

Authors:  Lim Heo; Collin F Arbour; Michael Feig
Journal:  Proteins       Date:  2019-06-24

9.  High-accuracy protein structures by combining machine-learning with physics-based refinement.

Authors:  Lim Heo; Michael Feig
Journal:  Proteins       Date:  2019-11-15

10.  Structure refinement of membrane proteins via molecular dynamics simulations.

Authors:  Bercem Dutagaci; Lim Heo; Michael Feig
Journal:  Proteins       Date:  2018-05-06
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