Mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data.

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

SUBMITTER: Perez-Hernandez G 

PROVIDER: S-EPMC12011235 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature