Literature DB >> 16683746

Molecular dynamics: survey of methods for simulating the activity of proteins.

Stewart A Adcock1, J Andrew McCammon.   

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Year:  2006        PMID： 16683746      PMCID： PMC2547409          DOI： 10.1021/cr040426m

Source DB:  PubMed          Journal:  Chem Rev        ISSN： 0009-2665            Impact factor:   60.622


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  194 in total

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2.  Developing a dynamic pharmacophore model for HIV-1 integrase.

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Journal:  J Med Chem       Date:  2000-06-01       Impact factor: 7.446

Review 3.  Molecular dynamics simulation of nucleic acids.

Authors:  T E Cheatham; P A Kollman
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

4.  The free energy landscape for beta hairpin folding in explicit water.

Authors:  R Zhou; B J Berne; R Germain
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5.  Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal.

Authors:  R Walser; P H Hünenberger; W F van Gunsteren
Journal:  Proteins       Date:  2001-06-01

6.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

7.  Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.

Authors:  Martin Zacharias
Journal:  Proteins       Date:  2004-03-01

8.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

Review 9.  Protein folding-simulation.

Authors:  Valerie Daggett
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

10.  Molecular dynamics simulation of the docking of substrates to proteins.

Authors:  A Di Nola; D Roccatano; H J Berendsen
Journal:  Proteins       Date:  1994-07
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  223 in total

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2.  Small molecules containing hetero-bicyclic ring systems compete with UDP-Glc for binding to WaaG glycosyltransferase.

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3.  Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

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4.  Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex.

Authors:  Nick S Laursen; Kasper R Andersen; Ingke Braren; Edzard Spillner; Lars Sottrup-Jensen; Gregers R Andersen
Journal:  EMBO J       Date:  2011-01-07       Impact factor: 11.598

5.  Shock Wave-Induced Damage of a Protein by Void Collapse.

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6.  Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations.

Authors:  Cong Zhao; Weihong Du
Journal:  J Biol Inorg Chem       Date:  2016-02-03       Impact factor: 3.358

7.  Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

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Journal:  Methods Enzymol       Date:  2015-02-07       Impact factor: 1.600

8.  Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?

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9.  Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation.

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Review 10.  Structure, mechanism, and dynamics of UDP-galactopyranose mutase.

Authors:  John J Tanner; Leonardo Boechi; J Andrew McCammon; Pablo Sobrado
Journal:  Arch Biochem Biophys       Date:  2013-10-03       Impact factor: 4.013
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