ProDy is a free and open-source Python package for analyzing protein structural dynamics. It allows for quantitative analysis of heterogeneous experimental structural datasets and comparison with theoretically predicted conformational dynamics. It is designed and developed by Ahmet Bakan in Bahar lab at the University of Pittsburgh.
The input for ProDy is the atomic coordinates of the query protein in PDB file format, or simply the PDB id or the single letter amino acid sequence of the protein. Fast and flexible ProDy parsers are used to retrieve the corresponding dataset of PDB files from the PDB FTP server and extract their coordinate data and other relevant information.
ProDy outputs the dominant patterns in structural variability extracted by principal component analysis (PCA) of the experimental datasets, and the normal modes describing the intrinsic dynamics of proteins predicted by normal mode analysis (NMA) based on elastic network models (ENMs).
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