{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T20:59:22Z","timestamp":1762981162973,"version":"3.37.3"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,21]],"date-time":"2021-07-21T00:00:00Z","timestamp":1626825600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Basis for Supporting Innovative Drug Discovery and Life Science Research"},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP18am0101114"],"award-info":[{"award-number":["JP18am0101114"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Comparing results from multiple MD simulations performed under different conditions is essential during the initial stages of analysis. We propose a tool called MD Contact Comparison (MDContactCom) that compares residue-residue contact fluctuations of two MD trajectories, quantifies the differences, identifies sites that exhibit large differences and visualizes those sites on the protein structure. Using this method, it is possible to identify sites affected by varying simulation conditions and reveal the path of propagation of the effect even when differences between the 3D structure of the molecule and the fluctuation RMSF of each residue is unclear. MDContactCom can monitor differences in complex protein dynamics between two MD trajectories and identify candidate sites to be analyzed in more detail. As such, MDContactCom is a versatile software package for analyzing most MD simulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MDContactCom is freely available for download on GitLab. The software is implemented in Python3. https:\/\/gitlab.com\/chiemotono\/mdcontactcom.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab538","type":"journal-article","created":{"date-parts":[[2021,7,20]],"date-time":"2021-07-20T11:09:39Z","timestamp":1626779379000},"page":"273-274","source":"Crossref","is-referenced-by-count":4,"title":["MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts"],"prefix":"10.1093","volume":"38","author":[{"given":"Chie","family":"Motono","sequence":"first","affiliation":[{"name":"Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo 135-0064, Japan"},{"name":"Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Waseda University , Tokyo 169-0072, Japan"}]},{"given":"Shunsuke","family":"Yanagida","sequence":"additional","affiliation":[{"name":"Bioscience & Healthcare Engineering Division, DX Infrastructure Engineering Unit 1, Mitsui Knowledge Industry Co., Ltd, Tokyo 164-0003, Japan"}]},{"given":"Miwa","family":"Sato","sequence":"additional","affiliation":[{"name":"Bioscience & Healthcare Engineering Division, DX Infrastructure Engineering Unit 1, Mitsui Knowledge Industry Co., Ltd, Tokyo 164-0003, Japan"}]},{"given":"Takatsugu","family":"Hirokawa","sequence":"additional","affiliation":[{"name":"Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo 135-0064, Japan"},{"name":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Ibaraki 305-8575, Japan"},{"name":"Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba , Ibaraki 305-8575, Japan"}]}],"member":"286","published-online":{"date-parts":[[2021,7,21]]},"reference":[{"key":"2023020108394105500_btab538-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1-2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2023020108394105500_btab538-B152","doi-asserted-by":"crossref","DOI":"10.1109\/SC.2006.54","article-title":"Scalable algorithms for molecular dynamics simulations on commodity clusters","author":"Bowers","year":"2006"},{"key":"2023020108394105500_btab538-B2","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: the biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J. 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