title: ProDy: protein dynamics inferred from theory and experiments.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.
authors.affiliation: Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA. ahb12@pitt.edu
authors.forename: Ahmet
authors.initials: A
authors.lastname: Bakan
authors.forename: Lidio M
authors.initials: LM
authors.lastname: Meireles
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
mesh_terms: D003196:Computer Graphics; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins