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Cited by 36Protein Structure and DynamicsReceptor Mechanisms and SignalingComputational Drug Discovery Methods

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mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data

Open access
Pérez-Hernández, Guillermo, Hildebrand, Peter W.·2025·PLOS Computational Biology
DOI 10.1371/journal.pcbi.1012837PMC PMC12011235

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Abstract

We present mdciao, an open-source command line tool and Python Application-Programming-Interface (API) for easy, one-shot analysis and representation of molecular dynamics (MD) simulation data. Building upon the widely used concept of residue-residue contact-frequencies, mdciao offers a wide spectrum of further analysis and representations, enriched with available domain specific annotations. The user-friendly interface offers pre-packaged solutions for non-expert users, while keeping customizability for expert ones. Emphasis has been put into automatically producing annotated, production-ready figures and tables. Furthermore, seamless on-the-fly query and inclusion of domain-specific generic residue numbering for GPCRs, GAIN-domains, G-proteins, and kinases is made possible through online lookups. This allows for easy selection and comparison across different systems, regardless of sequence identity, target residues or domains. Finally, the fully documented Python API allows users to include the basic or advanced mdciao functions in their analysis workflows, and provides numerous examples and Jupyter Notebook Tutorials. The source code is published under the GNU Lesser General Public License v3.0 or later and hosted on https://github.com/gph82/mdciao , and the documentation, including guides and examples, can be found at https://www.mdciao.org

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Metadata

Authors
Pérez-Hernández, G., & Hildebrand, P. W.
Affiliations
Humboldt-Universität zu Berlin (DE)
ORCID
Venue
PLOS Computational Biology
Publisher
Public Library of Science (PLoS)
Published
2025-04-21
Volume
21
Issue
4
Pages
e1012837
ISSN
  • 1553-734X (ISSN-L)
  • 1553-7358
DOI
10.1371/journal.pcbi.1012837
PMC
PMC12011235
OpenAlex
W4409640798
Cited by
36
References
3
Citations by year
2026: 9 · 2025: 16
FWCI
7.52
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Computational Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Deutsche Forschungsgemeinschaft (SFB1423, project 421152132, subproject C01 and Z04)
  • Stiftung Charité
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords
molecular dynamics simulation analysis, protein structure visualization, G protein-coupled receptors, G proteins, kinases, GAIN domain, Python interface, open source software
MeSH terms
Proteins, Software, User-Computer Interface, Computational Biology, Molecular Dynamics Simulation

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