Literature DB >> 18611844

Biomolecular simulation and modelling: status, progress and prospects.

Marc W van der Kamp1, Katherine E Shaw, Christopher J Woods, Adrian J Mulholland.   

Abstract

Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted.

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Year:  2008        PMID： 18611844      PMCID： PMC2706107          DOI： 10.1098/rsif.2008.0105.focus

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN： 1742-5662            Impact factor:   4.118


  164 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations.

Authors:  U Rothlisberger; P Carloni; K Doclo; M Parrinello
Journal:  J Biol Inorg Chem       Date:  2000-04       Impact factor: 3.358

3.  The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding.

Authors:  R B Von Dreele; P W Stephens; G D Smith; R H Blessing
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-12

4.  Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations.

Authors:  A Imberty; S Pérez
Journal:  Chem Rev       Date:  2000-12-13       Impact factor: 60.622

Review 5.  Quantum mechanical methods for enzyme kinetics.

Authors:  Jiali Gao; Donald G Truhlar
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

6.  Computer simulation of protein folding.

Authors:  M Levitt; A Warshel
Journal:  Nature       Date:  1975-02-27       Impact factor: 49.962

Review 7.  Molecular dynamics and NMR spin relaxation in proteins.

Authors:  David A Case
Journal:  Acc Chem Res       Date:  2002-06       Impact factor: 22.384

8.  Unified approach for molecular dynamics and density-functional theory.

Authors: 
Journal:  Phys Rev Lett       Date:  1985-11-25       Impact factor: 9.161

9.  A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent.

Authors:  H C Siebert; S André; J L Asensio; F J Cañada; X Dong; J F Espinosa; M Frank; M Gilleron; H Kaltner; T Kozár; N V Bovin; C W von Der Lieth; J F Vliegenthart; J Jiménez-Barbero; H J Gabius
Journal:  Chembiochem       Date:  2000-10-02       Impact factor: 3.164

10.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

Authors:  T E Cheatham; P Cieplak; P A Kollman
Journal:  J Biomol Struct Dyn       Date:  1999-02
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  10 in total

1.  Taking Ockham's razor to enzyme dynamics and catalysis.

Authors:  David R Glowacki; Jeremy N Harvey; Adrian J Mulholland
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

Review 2.  A practical guide to modelling enzyme-catalysed reactions.

Authors:  Richard Lonsdale; Jeremy N Harvey; Adrian J Mulholland
Journal:  Chem Soc Rev       Date:  2012-01-26       Impact factor: 54.564

3.  Introduction. Biomolecular simulation.

Authors:  Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

Review 4.  Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.

Authors:  Marco Pasi; Dimitar Angelov; Jan Bednar; Stefan Dimitrov; Richard Lavery
Journal:  Nucleus       Date:  2016-11       Impact factor: 4.197

5.  Dynameomics: a comprehensive database of protein dynamics.

Authors:  Marc W van der Kamp; R Dustin Schaeffer; Amanda L Jonsson; Alexander D Scouras; Andrew M Simms; Rudesh D Toofanny; Noah C Benson; Peter C Anderson; Eric D Merkley; Steven Rysavy; Dennis Bromley; David A C Beck; Valerie Daggett
Journal:  Structure       Date:  2010-03-14       Impact factor: 5.006

6.  Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics.

Authors:  David Parker; Zev Bryant; Scott L Delp
Journal:  Cell Mol Bioeng       Date:  2009-09-01       Impact factor: 2.321

7.  Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes.

Authors:  Mario Orsi; Massimo G Noro; Jonathan W Essex
Journal:  J R Soc Interface       Date:  2010-12-03       Impact factor: 4.118

Review 8.  Mathematical and computational modeling in biology at multiple scales.

Authors:  Jack A Tuszynski; Philip Winter; Diana White; Chih-Yuan Tseng; Kamlesh K Sahu; Francesco Gentile; Ivana Spasevska; Sara Ibrahim Omar; Niloofar Nayebi; Cassandra Dm Churchill; Mariusz Klobukowski; Rabab M Abou El-Magd
Journal:  Theor Biol Med Model       Date:  2014-12-27       Impact factor: 2.432

9.  Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

Authors:  Stephen A Wells; Marc W van der Kamp; John D McGeagh; Adrian J Mulholland
Journal:  PLoS One       Date:  2015-08-04       Impact factor: 3.240

10.  Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems.

Authors:  Romain Berraud-Pache; Cristina Garcia-Iriepa; Isabelle Navizet
Journal:  Front Chem       Date:  2018-04-17       Impact factor: 5.221
  10 in total

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