ProDy: protein dynamics inferred from theory and experiments. SUMMARY: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods. AVAILABILITY: ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.
Keywords for this software
References in zbMATH (referenced in 4 articles , 1 standard article )
Showing results 1 to 4 of 4.
- Nicolas Renaud; Cunliang Geng: The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries (2020) not zbMATH
- Sarkar, Ranja: Stiffening of flexible SUMO1 protein upon peptide-binding: analysis with anisotropic network model (2018)
- Berk Ekmekci, Charles E. McAnany, Cameron Mura: An Introduction to Programming for Bioscientists: A Python-based Primer (2016) arXiv
- Bakan, Ahmet; Meireles, Lidio M.; Bahar, Ivet: \textitprody: protein dynamics inferred from theory and experiments (2011) ioport