PyPCN: protein contact networks in PyMOL.

ABSTRACT:

Motivation

Protein contact networks (PCNs) represent the 3D structure of a protein using network formalism. Inter-residue contacts are described as binary adjacency matrices, which are derived from the graph representation of residues (as α-carbons, β-carbons or centroids) and Euclidean distances according to defined thresholds. Functional characterization algorithms are computed on binary adjacency matrices to unveil allosteric, dynamic, and interaction mechanisms in proteins. Such strategies are usually applied in a combinatorial manner, although rarely in seamless and user-friendly implementations.

Results

PyPCN is a plugin for PyMOL wrapping more than twenty PCN algorithms and metrics in an easy-to-use graphical user interface, to support PCN analysis. The plugin accepts

SUBMITTER: Rosignoli S 

PROVIDER: S-EPMC10641099 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature