Welcome to the xPyder download page!


xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by allowing extensive data filtering. xPyder includes a user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level.


The xPyder binary installers for Linux (32 or 64 bit), Windows and OS X can be downloaded here. Please consult the user manual and install the required software and libraries before installing xPyder. While the installers should work fine on most platforms, a plain compressed archive is also available to perform manual installation in case it was necessary.


The user manual is available here:

Additional software

Here are several useful scripts and utilities designed to easy the obtainment of xPyder-compatible input files.

Case study

We present here the test case of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis (AHA) and its mesophilic homolog pancreatic porcine amylase (PPA). Here you can download a dynamical cross correlation matrix (DCCM), which describes the correlated motions between alpha carbons of the proteins, both for AHA and PPA. A pdssp file, which describes the persistence degree of secondary structure in the MD simulation, and a dssp output file are also available. The data were calculated on full-atom molecular dynamics simulations. The crystal structure of AHA (1AQH) is also available to plot the correlations encoded by the matrices, as long as the dssp output file for 1AQH.


If you use xPyder for your scientific work, please cite the original scientific publication:

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.
Marco Pasi, Matteo Tiberti, Alberto Arrigoni, and Elena Papaleo
Journal of Chemical Information and Modeling 2012 52 (7), 1865-1874

See also

Interested in structural communication in protein systems? We have devised a software package designed to study structural communication in protein ensembles by analyzing non-covalent interactions between aminoacid side-chains and graph analysis. Nonetheless, it is designed to work in synergy with xPyder to deliver clear and beautiful representations of the collected data. For more information please visit the PyInteraph website.


You can contact the xPyder authors and developers at xpyder dot pymol at gmail dot com