MD-TASK: a software suite for analyzing molecular dynamics trajectories

Author:

Brown David K1,Penkler David L1,Sheik Amamuddy Olivier1,Ross Caroline1,Atilgan Ali Rana2,Atilgan Canan2,Tastan Bishop Özlem1

Affiliation:

1. Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa

2. Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey

Funder

National Institutes of Health

National Research Foundation

NRF

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Reference16 articles.

1. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin;Atilgan;J. Chem. Phys,2011

2. Network-based models as tools hinting at nonevident protein functionality;Atilgan;Annu. Rev. Biophys,2012

3. Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein;Atilgan;PLoS Comput. Biol,2009

4. An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine;Bhakat;Mol. Biosyst,2014

5. A faster algorithm for betweenness centrality*;Brandes;J. Math. Sociol,2001

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