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Published on: April 12, 2019
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.
Peter Schmidtke1, Axel Bidon-Chanal, F Javier Luque
1Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, 08028 Barcelona, Spain. pschmidtke@ub.edu
Bioinformatics (Oxford, England)
|October 5, 2011
Summary
MDpocket is a new, free tool that analyzes protein dynamics by tracking binding sites and pathways in molecular dynamics simulations. This open-source software enhances understanding of protein plasticity and function.
Area of Science:
- Biochemistry
- Computational Biology
- Structural Biology
Background:
- Existing protein pocket detection algorithms primarily analyze static structures.
- Proteins are dynamic entities, necessitating tools that account for conformational changes.
- Understanding protein plasticity is crucial for structure-function relationship insights.
Purpose of the Study:
- To introduce MDpocket, a novel, free, and open-source software.
- To enable the detection and characterization of protein cavities within dynamic conformational ensembles.
- To provide a tool for analyzing molecular dynamics (MD) trajectories and other ensembles.
Main Methods:
- MDpocket is based on the established fpocket cavity detection algorithm.
- The software tracks small molecule binding sites and gas migration pathways.
- It processes molecular dynamics (MD) trajectories and conformational ensembles.
Main Results:
- MDpocket successfully detected transient subpockets in HSP90 crystal structures.
- It identified known xenon binding sites and migration pathways in myoglobin.
- The tool identified suitable pockets for molecular docking in P38 Map kinase.
Conclusions:
- MDpocket offers a valuable, fast, and open-source solution for analyzing protein pocket dynamics.
- The software aids in capturing protein plasticity and understanding structure-function relationships.
- It serves as a significant contribution to the field of computational structural biology.
