Literature DB >> 15663003

Interactive essential dynamics.

John Mongan1.   

Abstract

Essential dynamics (ED) is a useful method for analyzing trajectories generated by molecular dynamics (MD), but current tools are awkward to use, limiting the usefulness of the technique. This paper describes a new interactive graphical interface for visualization of ED results, including filtering a trajectory on an arbitrary set of eigenvectors and manipulation of a structure's projection along any eigenvector.

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Year:  2004        PMID： 15663003     DOI： 10.1007/s10822-004-4121-z

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  11 in total

1.  Concerted motions in copper plastocyanin and azurin: an essential dynamics study.

Authors:  C Arcangeli; A R Bizzarri; S Cannistraro
Journal:  Biophys Chem       Date:  2001-03-15       Impact factor: 2.352

2.  Computational studies of essential dynamics of Pseudomonas cepacia lipase.

Authors:  J Lee; S W Suh; S Shin
Journal:  J Biomol Struct Dyn       Date:  2000-10

3.  Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

Authors:  B L de Groot; X Daura; A E Mark; H Grubmüller
Journal:  J Mol Biol       Date:  2001-05-25       Impact factor: 5.469

4.  Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

Authors:  Donald Hamelberg; John Mongan; J Andrew McCammon
Journal:  J Chem Phys       Date:  2004-06-22       Impact factor: 3.488

5.  WHAT IF: a molecular modeling and drug design program.

Authors:  G Vriend
Journal:  J Mol Graph       Date:  1990-03

6.  Large-amplitude nonlinear motions in proteins.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-04-27       Impact factor: 9.161

7.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

8.  Essential dynamics of proteins.

Authors:  A Amadei; A B Linssen; H J Berendsen
Journal:  Proteins       Date:  1993-12

9.  Use of essential and molecular dynamics to study gammaB-crystallin unfolding after non-enzymic post-translational modifications.

Authors:  M James C Crabbe; Lee R Cooper; David W Corne
Journal:  Comput Biol Chem       Date:  2003-10       Impact factor: 2.877

10.  Conformational flexibility of beta-secretase: molecular dynamics simulation and essential dynamics analysis.

Authors:  Bin Xiong; Xiao-Qin Huang; Ling-Ling Shen; Jian-Hua Shen; Xiao-Min Luo; Xu Shen; Hua-Liang Jiang; Kai-Xian Chen
Journal:  Acta Pharmacol Sin       Date:  2004-06       Impact factor: 6.150
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  28 in total

1.  Exploring global motions and correlations in the ribosome.

Authors:  Joanna Trylska; Valentina Tozzini; J Andrew McCammon
Journal:  Biophys J       Date:  2005-06-10       Impact factor: 4.033

2.  Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin.

Authors:  Mathew Varghese Koonammackal; Unnikrishnan Viswambharan Nair Nellipparambil; Chellappanpillai Sudarsanakumar
Journal:  J Mol Model       Date:  2011-02-02       Impact factor: 1.810

3.  Collective dynamics of periplasmic glutamine binding protein upon domain closure.

Authors:  Hannes H Loeffler; Akio Kitao
Journal:  Biophys J       Date:  2009-11-04       Impact factor: 4.033

4.  Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling.

Authors:  Yunierkis Pérez-Castillo; Matheus Froeyen; Miguel Angel Cabrera-Pérez; Ann Nowé
Journal:  J Comput Aided Mol Des       Date:  2011-04-23       Impact factor: 3.686

5.  Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1.

Authors:  Chunli Yan; Tamer Kaoud; Sunbae Lee; Kevin N Dalby; Pengyu Ren
Journal:  J Phys Chem B       Date:  2011-01-25       Impact factor: 2.991

6.  Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein.

Authors:  Raudah Lazim; Ye Mei; Dawei Zhang
Journal:  J Mol Model       Date:  2011-06-14       Impact factor: 1.810

7.  Using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes P450.

Authors:  Yergalem T Meharenna; Thomas L Poulos
Journal:  Biochemistry       Date:  2010-08-10       Impact factor: 3.162

8.  Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case.

Authors:  Peter M U Ung; Phani Ghanakota; Sarah E Graham; Katrina W Lexa; Heather A Carlson
Journal:  Biopolymers       Date:  2016-01       Impact factor: 2.505

9.  Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics.

Authors:  Monique Laberge; Takashi Yonetani
Journal:  Biophys J       Date:  2007-12-20       Impact factor: 4.033

10.  Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.

Authors:  Kamila Réblová; Filip Rázga; Wen Li; Haixiao Gao; Joachim Frank; Jirí Sponer
Journal:  Nucleic Acids Res       Date:  2009-12-01       Impact factor: 16.971
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