{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T16:02:18Z","timestamp":1775750538412,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,5,31]],"date-time":"2017-05-31T00:00:00Z","timestamp":1496188800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U41HG006941 to H3ABioNet"],"award-info":[{"award-number":["U41HG006941 to H3ABioNet"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011512","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011512","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007431","name":"NRF","doi-asserted-by":"publisher","award":["93690"],"award-info":[{"award-number":["93690"]}],"id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MD-TASK has been open-sourced and is available for download from https:\/\/github.com\/RUBi-ZA\/MD-TASK, implemented in Python and supported on Linux\/Unix.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx349","type":"journal-article","created":{"date-parts":[[2017,5,30]],"date-time":"2017-05-30T11:21:29Z","timestamp":1496143289000},"page":"2768-2771","source":"Crossref","is-referenced-by-count":198,"title":["MD-TASK: a software suite for analyzing molecular dynamics trajectories"],"prefix":"10.1093","volume":"33","author":[{"given":"David K","family":"Brown","sequence":"first","affiliation":[{"name":"Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa"}]},{"given":"David L","family":"Penkler","sequence":"additional","affiliation":[{"name":"Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa"}]},{"given":"Olivier","family":"Sheik Amamuddy","sequence":"additional","affiliation":[{"name":"Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa"}]},{"given":"Caroline","family":"Ross","sequence":"additional","affiliation":[{"name":"Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa"}]},{"given":"Ali Rana","family":"Atilgan","sequence":"additional","affiliation":[{"name":"Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey"}]},{"given":"Canan","family":"Atilgan","sequence":"additional","affiliation":[{"name":"Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey"}]},{"given":"\u00d6zlem","family":"Tastan Bishop","sequence":"additional","affiliation":[{"name":"Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa"}]}],"member":"286","published-online":{"date-parts":[[2017,5,31]]},"reference":[{"key":"2023020206261471000_btx349-B1","doi-asserted-by":"crossref","DOI":"10.1063\/1.3651807","article-title":"Subtle pH differences trigger single residue motions for moderating conformations of calmodulin","volume":"135","author":"Atilgan","year":"2011","journal-title":"J. Chem. Phys"},{"key":"2023020206261471000_btx349-B2","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1146\/annurev-biophys-050511-102305","article-title":"Network-based models as tools hinting at nonevident protein functionality","volume":"41","author":"Atilgan","year":"2012","journal-title":"Annu. Rev. Biophys"},{"key":"2023020206261471000_btx349-B3","doi-asserted-by":"crossref","first-page":"10005","DOI":"10.1371\/journal.pcbi.1000544","article-title":"Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein","volume":"5","author":"Atilgan","year":"2009","journal-title":"PLoS Comput. Biol"},{"key":"2023020206261471000_btx349-B4","doi-asserted-by":"crossref","first-page":"2215","DOI":"10.1039\/C4MB00253A","article-title":"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","volume":"10","author":"Bhakat","year":"2014","journal-title":"Mol. Biosyst"},{"key":"2023020206261471000_btx349-B5","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1080\/0022250X.2001.9990249","article-title":"A faster algorithm for betweenness centrality*","volume":"25","author":"Brandes","year":"2001","journal-title":"J. Math. Sociol"},{"key":"2023020206261471000_btx349-B6","doi-asserted-by":"crossref","DOI":"10.1016\/j.gheart.2017.01.006","article-title":"Structure-based analysis of single nucleotide variants in the renin-angiotensinogen complex","author":"Brown","year":"2017","journal-title":"Glob. Heart"},{"key":"2023020206261471000_btx349-B7","doi-asserted-by":"crossref","DOI":"10.1016\/j.gheart.2017.01.009","article-title":"Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis","author":"Brown","year":"2017","journal-title":"Glob. Heart"},{"key":"2023020206261471000_btx349-B8","doi-asserted-by":"crossref","first-page":"4735","DOI":"10.1073\/pnas.1523573113","article-title":"Dynamical network of residue\u2013residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation","volume":"113","author":"Doshi","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020206261471000_btx349-B9","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: A 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng"},{"key":"2023020206261471000_btx349-B10","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/ar000033j","article-title":"Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models","volume":"33","author":"Kollman","year":"2000","journal-title":"Acc. Chem. Res"},{"key":"2023020206261471000_btx349-B11","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1002\/prot.24734","article-title":"Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: a computational study","volume":"83","author":"Di Marino","year":"2015","journal-title":"Proteins"},{"key":"2023020206261471000_btx349-B12","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1016\/j.str.2005.11.005","article-title":"Wide-Open\u2019 structure of a multidrug-resistant HIV-1 protease as a drug target","volume":"13","author":"Martin","year":"2017","journal-title":"Structure"},{"key":"2023020206261471000_btx349-B13","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1016\/j.bpj.2015.08.015","article-title":"MDTraj: a modern open library for the analysis of molecular dynamics trajectories","volume":"109","author":"McGibbon","year":"2015","journal-title":"Biophys. J"},{"key":"2023020206261471000_btx349-B14","author":"NetworkX Developers","year":"2017"},{"key":"2023020206261471000_btx349-B15","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.1002\/prot.24925","article-title":"In silico mutational studies of Hsp70 disclose sites with distinct functional attributes","volume":"83","author":"Ozbaykal","year":"2015","journal-title":"Proteins"},{"key":"2023020206261471000_btx349-B16","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jcim.6b00775","article-title":"Perturbation response scanning reveals key residues for allosteric control in Hsp70","author":"Penkler","year":"2017","journal-title":"J. Chem. Inf. Model"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2768\/49040614\/bioinformatics_33_17_2768.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2768\/49040614\/bioinformatics_33_17_2768.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:28:18Z","timestamp":1675319298000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/17\/2768\/3859177"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,31]]},"references-count":16,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2017,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx349","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,9,1]]},"published":{"date-parts":[[2017,5,31]]}}}