Literature DB >> 25606670

Beating the millisecond barrier in molecular dynamics simulations.

Frank Noé1.   

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Year:  2015        PMID: 25606670      PMCID: PMC4302188          DOI: 10.1016/j.bpj.2014.11.3477

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


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  12 in total

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2.  Atomic-level characterization of the structural dynamics of proteins.

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3.  Error analysis and efficient sampling in Markovian state models for molecular dynamics.

Authors:  Nina Singhal; Vijay S Pande
Journal:  J Chem Phys       Date:  2005-11-22       Impact factor: 3.488

4.  Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.

Authors:  Daniel L Ensign; Peter M Kasson; Vijay S Pande
Journal:  J Mol Biol       Date:  2007-09-29       Impact factor: 5.469

5.  Ten-microsecond molecular dynamics simulation of a fast-folding WW domain.

Authors:  Peter L Freddolino; Feng Liu; Martin Gruebele; Klaus Schulten
Journal:  Biophys J       Date:  2008-03-13       Impact factor: 4.033

6.  Adaptive single replica multiple state transition interface sampling.

Authors:  Wei-Na Du; Peter G Bolhuis
Journal:  J Chem Phys       Date:  2013-07-28       Impact factor: 3.488

7.  Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

Authors:  Ignasi Buch; Toni Giorgino; Gianni De Fabritiis
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-06       Impact factor: 11.205

8.  Equilibrium kinetic network of the villin headpiece in implicit solvent.

Authors:  Weina Du; Peter G Bolhuis
Journal:  Biophys J       Date:  2015-01-20       Impact factor: 4.033

9.  Kinetic characterization of the critical step in HIV-1 protease maturation.

Authors:  S Kashif Sadiq; Frank Noé; Gianni De Fabritiis
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-26       Impact factor: 11.205

10.  Activation pathway of Src kinase reveals intermediate states as targets for drug design.

Authors:  Diwakar Shukla; Yilin Meng; Benoît Roux; Vijay S Pande
Journal:  Nat Commun       Date:  2014-03-03       Impact factor: 14.919

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  7 in total

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2.  Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge.

Authors:  Ryan L Melvin; Ryan C Godwin; Jiajie Xiao; William G Thompson; Kenneth S Berenhaut; Freddie R Salsbury
Journal:  J Chem Theory Comput       Date:  2016-11-10       Impact factor: 6.006

Review 3.  In Silico Strategies in Tuberculosis Drug Discovery.

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Review 4.  Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

Authors:  Jeffrey R Wagner; Christopher T Lee; Jacob D Durrant; Robert D Malmstrom; Victoria A Feher; Rommie E Amaro
Journal:  Chem Rev       Date:  2016-04-13       Impact factor: 60.622

Review 5.  Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.

Authors:  Bartłomiej Surpeta; Carlos Eduardo Sequeiros-Borja; Jan Brezovsky
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Review 6.  Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.

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Review 7.  Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach.

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  7 in total

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