mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data

Abstract

We present mdciao, an open-source command line tool and Python Application-Programmers-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 domain specific annotations when possible. It tries offer a user-friendly interface, which simplifies most decisions for non-expert users, while keeping customizability for expert ones. Emphasis has been put into automatically producing annotated, paper-ready figures and tables. Furthermore, seamless on-the-fly query and inclusion of consensus nomenclatures for GPCR, G-proteins, and kinases is made possible through the respective online databases, which allows for bulk selection and comparison across different systems. 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.