Academic Journal
MDCompress: better, faster compression of molecular dynamics simulation trajectories.
| Title: | MDCompress: better, faster compression of molecular dynamics simulation trajectories. |
|---|---|
| Authors: | Kokot, Marek, Roy, Amitava, Wheeler, Travis J, Deorowicz, Sebastian |
| Source: | Bioinformatics; Apr2026, Vol. 42 Issue 4, p1-11, 11p |
| Subject Terms: | Molecular dynamics, Data compression, Simultaneous multithreading processors, Trajectories (Mechanics), Computer software execution |
| Abstract: | Motivation 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. Results Here, we introduce MDCompress, a new trajectory compression format and accompanying software implementation that meets these goals. MDCompress produces compressed trajectory files that are 15–37% smaller than those generated by the widely-used XTC format, while achieving faster compression and decompression speeds through efficient multithreading. Availability and implementation 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 [ABSTRACT FROM AUTHOR] |
| Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Complementary Index |
| FullText | Links: – Type: other Text: Availability: 0 |
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| Header | DbId: edb DbLabel: Complementary Index An: 193500436 RelevancyScore: 1061 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 1060.75964355469 |
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| Items | – Name: Title Label: Title Group: Ti Data: MDCompress: better, faster compression of molecular dynamics simulation trajectories. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Kokot%2C+Marek%22">Kokot, Marek</searchLink><br /><searchLink fieldCode="AR" term="%22Roy%2C+Amitava%22">Roy, Amitava</searchLink><br /><searchLink fieldCode="AR" term="%22Wheeler%2C+Travis+J%22">Wheeler, Travis J</searchLink><br /><searchLink fieldCode="AR" term="%22Deorowicz%2C+Sebastian%22">Deorowicz, Sebastian</searchLink> – Name: TitleSource Label: Source Group: Src Data: Bioinformatics; Apr2026, Vol. 42 Issue 4, p1-11, 11p – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Data+compression%22">Data compression</searchLink><br /><searchLink fieldCode="DE" term="%22Simultaneous+multithreading+processors%22">Simultaneous multithreading processors</searchLink><br /><searchLink fieldCode="DE" term="%22Trajectories+%28Mechanics%29%22">Trajectories (Mechanics)</searchLink><br /><searchLink fieldCode="DE" term="%22Computer+software+execution%22">Computer software execution</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Motivation 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. Results Here, we introduce MDCompress, a new trajectory compression format and accompanying software implementation that meets these goals. MDCompress produces compressed trajectory files that are 15–37% smaller than those generated by the widely-used XTC format, while achieving faster compression and decompression speeds through efficient multithreading. Availability and implementation 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 [ABSTRACT FROM AUTHOR] – Name: Abstract Label: Group: Ab Data: <i>Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1093/bioinformatics/btag176 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 1 Subjects: – SubjectFull: Molecular dynamics Type: general – SubjectFull: Data compression Type: general – SubjectFull: Simultaneous multithreading processors Type: general – SubjectFull: Trajectories (Mechanics) Type: general – SubjectFull: Computer software execution Type: general Titles: – TitleFull: MDCompress: better, faster compression of molecular dynamics simulation trajectories. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Kokot, Marek – PersonEntity: Name: NameFull: Roy, Amitava – PersonEntity: Name: NameFull: Wheeler, Travis J – PersonEntity: Name: NameFull: Deorowicz, Sebastian IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 04 Text: Apr2026 Type: published Y: 2026 Identifiers: – Type: issn-print Value: 13674803 Numbering: – Type: volume Value: 42 – Type: issue Value: 4 Titles: – TitleFull: Bioinformatics Type: main |
| ResultId | 1 |