Literature DB >> 12601794

Molecular dynamics of biological macromolecules: a brief history and perspective.

Martin Karplus1.   

Abstract

A description of the origin of my interest in and the development of molecular dynamics simulations of biomolecules is presented with a historical overview, including the role of my interactions with Shneior Lifson and his group in Israel. Some early applications of the methodology by members of my group are summarized, followed by a description of examples of recent applications and some discussion of possible future directions. Copyright 2003 Wiley Periodicals, Inc. Biopolymers: 350-358, 2003

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Year:  2003        PMID: 12601794     DOI: 10.1002/bip.10266

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  19 in total

1.  How an enzyme surmounts the activation energy barrier.

Authors:  Richard L Schowen
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-06       Impact factor: 11.205

Review 2.  Integrated Modeling Program, Applied Chemical Theory (IMPACT).

Authors:  Jay L Banks; Hege S Beard; Yixiang Cao; Art E Cho; Wolfgang Damm; Ramy Farid; Anthony K Felts; Thomas A Halgren; Daniel T Mainz; Jon R Maple; Robert Murphy; Dean M Philipp; Matthew P Repasky; Linda Y Zhang; Bruce J Berne; Richard A Friesner; Emilio Gallicchio; Ronald M Levy
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  Comparative study of generalized Born models: protein dynamics.

Authors:  Hao Fan; Alan E Mark; Jiang Zhu; Barry Honig
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-06       Impact factor: 11.205

4.  Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch.

Authors:  Senthil K Kandasamy; Ronald G Larson
Journal:  Biophys J       Date:  2006-01-20       Impact factor: 4.033

Review 5.  Protein dynamics via computational microscope.

Authors:  Anton B Guliaev; Senping Cheng; Bo Hang
Journal:  World J Methodol       Date:  2012-12-26

6.  Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process.

Authors:  Igor V Kurnikov; Maria Kurnikova
Journal:  J Phys Chem B       Date:  2015-07-31       Impact factor: 2.991

7.  Electrostatics of Cytochrome-c assemblies.

Authors:  V Renugopalakrishnan; Miguel Ortiz-Lombardía; Chandra Verma
Journal:  J Mol Model       Date:  2005-05-03       Impact factor: 1.810

Review 8.  Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.

Authors:  R Bryn Fenwick; Santi Esteban-Martín; Xavier Salvatella
Journal:  Eur Biophys J       Date:  2011-11-17       Impact factor: 1.733

9.  Investigation by MD simulation of the key residues related to substrate-binding and heme-release in human ferrochelatase.

Authors:  Yaxue Wang; Jingheng Wu; Jinqian Ju; Yong Shen
Journal:  J Mol Model       Date:  2013-02-28       Impact factor: 1.810

10.  Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics.

Authors:  Patricia Amara; Laurence Serre; Bertrand Castaing; Aline Thomas
Journal:  Protein Sci       Date:  2004-08       Impact factor: 6.725

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