Literature DB >> 7648323

Methodological advances in molecular dynamics simulations of biological systems.

C L Brooks1.   

Abstract

New advances in the techniques used to simulate specific statistical ensembles provide molecular dynamics algorithms that permit rigorous connections to be made between thermodynamic observables and calculated quantities in simulations of biological molecules. The complete inclusion of electrostatic forces in simulations also improves the comparison between calculations of simple structural measures in crystals and X-ray crystallographic results. These advances coupled with the ongoing development of more accurate inter/intramolecular forcefields with enhanced accuracy provide guidelines and benchmarks for comparison as we move to study more complicated biological problems.

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Year:  1995        PMID: 7648323     DOI: 10.1016/0959-440x(95)80078-6

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


  8 in total

1.  De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.

Authors:  D Mohanty; A Kolinski; J Skolnick
Journal:  Biophys J       Date:  1999-07       Impact factor: 4.033

2.  Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

Authors:  Sinan Keten; Markus J Buehler
Journal:  J R Soc Interface       Date:  2010-06-02       Impact factor: 4.118

3.  Calculation of electron paramagnetic resonance spectra from Brownian dynamics trajectories: application to nitroxide side chains in proteins.

Authors:  H J Steinhoff; W L Hubbell
Journal:  Biophys J       Date:  1996-10       Impact factor: 4.033

4.  Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.

Authors:  L S Caves; J D Evanseck; M Karplus
Journal:  Protein Sci       Date:  1998-03       Impact factor: 6.725

5.  Nanoconfinement controls stiffness, strength and mechanical toughness of beta-sheet crystals in silk.

Authors:  Sinan Keten; Zhiping Xu; Britni Ihle; Markus J Buehler
Journal:  Nat Mater       Date:  2010-03-14       Impact factor: 43.841

Review 6.  Selected new developments in computational chemistry.

Authors:  T A Darden; L Bartolotti; L G Pedersen
Journal:  Environ Health Perspect       Date:  1996-03       Impact factor: 9.031

7.  Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Comput Chem       Date:  2008-09       Impact factor: 3.376

8.  Inactivation and secondary structure in the D4/S4-5 region of the SkM1 sodium channel.

Authors:  G N Filatov; T P Nguyen; S D Kraner; R L Barchi
Journal:  J Gen Physiol       Date:  1998-06       Impact factor: 4.086

  8 in total

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