Content area

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

Details

1009240
Company / organization
Title
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data
Publication title
Volume
21
Issue
4
First page
e1012837
Number of pages
18
Publication year
2025
Publication date
Apr 2025
Section
Software
Publisher
Public Library of Science
Place of publication
San Francisco
Country of publication
United States
Publication subject
ISSN
1553734X
e-ISSN
15537358
Source type
Scholarly Journal
Language of publication
English
Document type
Journal Article
Publication history
 
 
Milestone dates
2024-10-22 (Received); 2025-01-31 (Accepted); 2025-04-21 (Published)
ProQuest document ID
3270580104
Document URL
https://www.proquest.com/scholarly-journals/mdciao-accessible-analysis-visualization/docview/3270580104/se-2?accountid=208611
Copyright
© 2025 Pérez-Hernández, Hildebrand. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Last updated
2025-11-11
Database
2 databases
  • Coronavirus Research Database
  • ProQuest One Academic