IMPORTANT: The tool is no longer maintained by us and we are looking for solutions to replace its functionalities within Pyinteraph2: https://github.com/ELELAB/pyinteraph2
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 from our github repository github repository, where you can find:
- the installation packages for Windows, Linux and OS X, as well as a tarball package inside the "packages" directory
- the xPyder user manual under the "docs" directory
- scripts and source files inside the "scripts" directory, in particular:
- t_dssp - converts the xpm matrix format, derived by the GROMACS's do_dssp tool, and the dssp output format to the PDSSP format
- wordomddcm2dat - converts Wordom's DCCM format to the xPyder .dat format
- wordompsn2dat - converts Wordom's PSN data to the xPyder .dat format
- theseusdccm2dat - converts Theseus matrix data to xPyder.dat
- theseuspcs2dat - plot Theseus-derived PCs in the diagonal of an empty xPyder matrix
- nmrsplit - split multi-model NMR pdbs into single PDB files, one model per file
- deltamat - compare symmetrical matrices derived from atomistic simulations
- A test case of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis (AHA) and its mesophilic homolog pancreatic porcine amylase (PPA). From the "example" directory you can download a dynamical cross correlation matrix (DCCM), which describes the correlated motions between alpha carbons of the proteins, for both 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 well as the dssp output file for 1AQH.
If you use xPyder in a scientific publication please cite the original source:
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
If you use deltamat for your scientific work, please cite:
A (dis)similarity index to compare correlated motions in molecular simulations.
Matteo Tiberti, Gaetano Invernizzi and Elena Papaleo
Accepted for publication on JCTC
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 repository.
You can contact the xPyder authors and developers at xpyder dot pymol at gmail dot com