{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,26]],"date-time":"2026-04-26T21:33:57Z","timestamp":1777239237633,"version":"3.51.4"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004442","name":"National Science Centre, Poland","doi-asserted-by":"publisher","award":["DEC-2022\/45\/B\/ST6\/03032"],"award-info":[{"award-number":["DEC-2022\/45\/B\/ST6\/03032"]}],"id":[{"id":"10.13039\/501100004442","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Molecular dynamics (MD) simulations model the physical movements of atoms in biomolecular systems over time, providing atomic-resolution insight into conformational changes, binding events, and dynamic behaviors that cannot be captured by static structures alone. As such, MD simulations are playing an increasingly important role in understanding the functional roles and molecular interactions of proteins. However, trajectories from these simulations can be extremely large, often reaching tens of gigabytes for a single simulation of modest duration. This creates substantial challenges for storage and data transfer, motivating efficient compression strategies. Furthermore, many downstream analyses require extraction of only a subset of frames or specific atoms from the full trajectory, so an ideal compression format should support rapid random-access decompression of such samplings without requiring full file decompression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we introduce MDCompress, a new trajectory compression format and accompanying software implementation that meets these goals. MDCompress produces compressed trajectory files that are 15\u201337% smaller than those generated by the widely-used XTC format, while achieving faster compression and decompression speeds through efficient multithreading.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The MDCompress software and library are released under an open license (BSD-3) and may be downloaded at https:\/\/github.com\/refresh-bio\/mdcompress and is also available as a Zenodo repository at 10.5281\/zenodo.19218347<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag176","type":"journal-article","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T11:42:25Z","timestamp":1775821345000},"source":"Crossref","is-referenced-by-count":0,"title":["MDCompress: better, faster compression of molecular dynamics simulation trajectories"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6420-1587","authenticated-orcid":false,"given":"Marek","family":"Kokot","sequence":"first","affiliation":[{"name":"Department of Algorithmics and Software, Silesian University of Technology , Gliwice, 44100,","place":["Poland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amitava","family":"Roy","sequence":"additional","affiliation":[{"name":"Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT, 59812,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2004-1785","authenticated-orcid":false,"given":"Travis J","family":"Wheeler","sequence":"additional","affiliation":[{"name":"College of Pharmacy, University of Arizona , Tucson, AZ, 85721,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9496-733X","authenticated-orcid":false,"given":"Sebastian","family":"Deorowicz","sequence":"additional","affiliation":[{"name":"Department of Algorithmics and Software, Silesian University of Technology , Gliwice, 44100,","place":["Poland"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,4,10]]},"reference":[{"key":"2026042616415563700_btag176-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","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2026042616415563700_btag176-B2","doi-asserted-by":"crossref","first-page":"D393","DOI":"10.1093\/nar\/gkad991","article-title":"A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort","volume":"52","author":"Beltr\u00e1n","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026042616415563700_btag176-B3","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1017\/S0033583525000034","article-title":"Protein Data Bank (PDB): fifty-three years young and having a transformative impact on science and society","volume":"58","author":"Berman","year":"2025","journal-title":"Q Rev Biophys"},{"key":"2026042616415563700_btag176-B4","doi-asserted-by":"crossref","first-page":"7835","DOI":"10.1021\/acs.jcim.5c01063","article-title":"Recent developments in amber biomolecular simulations","volume":"65","author":"Case","year":"2025","journal-title":"J Chem Inf Model"},{"key":"2026042616415563700_btag176-B5","doi-asserted-by":"crossref","first-page":"btae428","DOI":"10.1093\/bioinformatics\/btae428","article-title":"Efficient protein structure archiving using ProteStAr","volume":"40","author":"Deorowicz","year":"2024","journal-title":"Bioinformatics"},{"key":"2026042616415563700_btag176-B6","doi-asserted-by":"crossref","first-page":"107531","DOI":"10.1016\/j.jmgm.2020.107531","article-title":"Predictive compression of molecular dynamics trajectories","volume":"96","author":"Dvo\u0159\u00e1k","year":"2020","journal-title":"J Mol Graph Model"},{"key":"2026042616415563700_btag176-B7","unstructured":"Fraux G, Kimms L, Fine J \u00a0et al \u00a0chemfiles\/chemfiles: Version 0.10.4. 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