Literature DB >> 11525172

Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work.

T Schlick1.   

Abstract

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Year:  2001        PMID： 11525172     DOI： 10.1016/s0969-2126(01)00593-7

Source DB:  PubMed          Journal:  Structure        ISSN： 0969-2126            Impact factor:   5.006


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  8 in total

1.  A Hoogsteen base pair embedded in undistorted B-DNA.

Authors:  Jun Aishima; Rossitza K Gitti; Joyce E Noah; Hin Hark Gan; Tamar Schlick; Cynthia Wolberger
Journal:  Nucleic Acids Res       Date:  2002-12-01       Impact factor: 16.971

2.  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

3.  Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion.

Authors:  Jing Huang; Qing Zhang; Tamar Schlick
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

4.  Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass.

Authors:  Yanli Wang; Karunesh Arora; Tamar Schlick
Journal:  Protein Sci       Date:  2005-12-01       Impact factor: 6.725

5.  Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.

Authors:  Yanli Wang; Sujatha Reddy; William A Beard; Samuel H Wilson; Tamar Schlick
Journal:  Biophys J       Date:  2007-02-09       Impact factor: 4.033

6.  Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

Authors:  Linjing Yang; William A Beard; Samuel H Wilson; Suse Broyde; Tamar Schlick
Journal:  Biophys J       Date:  2004-06       Impact factor: 4.033

Review 7.  Molecular dynamics: survey of methods for simulating the activity of proteins.

Authors:  Stewart A Adcock; J Andrew McCammon
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

8.  Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides.

Authors:  Yanli Wang; Tamar Schlick
Journal:  BMC Struct Biol       Date:  2007-02-21
  8 in total

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