ProDy 1.5.1

Open source Python package for protein structural dynamics analysis
ProDy is designed for structure-based analysis of protein dynamics. It allows for quantitative analysis of heterogeneous experimental structural datasets and comparison with theoretically predicted conformational dynamics.

Experimental datasets include structural ensembles composed of sequence homologs, orthologs, mutant forms of a protein in the presence/absence of their substrates, ligands or inhibitors. Dominant patterns in structural variability are extracted by principal component analysis (PCA) of the datasets of structures.

On the theoretical side, protein dynamics is predicted using normal mode analysis (NMA) based on elastic network models (ENMs) or is extracted from molecular dynamics (MD) trajectories using essential dynamics analysis (EDA). Numerous helper functions enable comparative analysis of thus obtained experimental and theoretical data, and visualize the principal changes in conformations that are accessible in different functional states.

In the interactive usage examples throughout the documentation, the input is the set of atomic coordinates of the query protein in PDB file format, or simply the PDB id or 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 the coordinate data and other relevant information.

Results from PCA and NMA calculations can be plotted and saved as high-quality image files or visualized in VMD using NMWiz plug-in. In addition, ProDy allows for comparative analysis of PCA, NMA, or EDA results generated by other software. User can input normal mode data in plain text files to use the rich library of analysis and plotting functions

  ProDy is an 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.

Get ProDy and take it for a test drive to fully asses its capabilities!

last updated on:
August 6th, 2014, 22:47 GMT
file size:
1.1 MB
price:
FREE!
developed by:
Ahmet Bakan
license type:
GPL 
operating system(s):
Windows All
category:
C: \ Science / CAD

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