Literature DB >> 10753819

Long timescale simulations.

V Daggett1.   

Abstract

Computers are becoming increasingly fast, making it possible to perform simulations of macromolecules on timescales that were previously inaccessible. Questions have arisen concerning how well we are keeping up with computer power and the state of the art with respect to long molecular dynamics simulations in solvent. More importantly, however, simulations of macromolecules are performed to aid the understanding of biochemical phenomena. So, what are we learning from longer simulations and are they providing reliable insight into protein dynamics, conformational behavior and function?

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Year:  2000        PMID: 10753819     DOI: 10.1016/s0959-440x(00)00062-2

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


  25 in total

Review 1.  Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.

Authors:  C Vieille; G J Zeikus
Journal:  Microbiol Mol Biol Rev       Date:  2001-03       Impact factor: 11.056

2.  Ultrafast folding of WW domains without structured aromatic clusters in the denatured state.

Authors:  N Ferguson; C M Johnson; M Macias; H Oschkinat; A Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2001-10-30       Impact factor: 11.205

3.  Enzymology. A moving story.

Authors:  Joseph J Falke
Journal:  Science       Date:  2002-02-22       Impact factor: 47.728

4.  A model of the pressure dependence of the enantioselectivity of Candida rugosalipase towards (+/-)-menthol.

Authors:  U H Kahlow; R D Schmid; J Pleiss
Journal:  Protein Sci       Date:  2001-10       Impact factor: 6.725

5.  Simulations of human lysozyme: probing the conformations triggering amyloidosis.

Authors:  George Moraitakis; Julia M Goodfellow
Journal:  Biophys J       Date:  2003-04       Impact factor: 4.033

6.  Molecular dynamics simulations of peptides and proteins with amplified collective motions.

Authors:  Zhiyong Zhang; Yunyu Shi; Haiyan Liu
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

7.  Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms.

Authors:  Tamar Schlick
Journal:  Biophys J       Date:  2003-07       Impact factor: 4.033

8.  Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing.

Authors:  Ravi Radhakrishnan; Tamar Schlick
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-06       Impact factor: 11.205

9.  Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations.

Authors:  Pau Bernadó; Miguel X Fernandes; Doris M Jacobs; Klaus Fiebig; José García de la Torre; Miquel Pons
Journal:  J Biomol NMR       Date:  2004-05       Impact factor: 2.835

10.  Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli.

Authors:  Naser Alijabbari; Yikan Chen; Igor Sizov; Tatiana Globus; Boris Gelmont
Journal:  J Mol Model       Date:  2011-09-27       Impact factor: 1.810

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