PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins

TY - JOUR

T1 - PyInteraph

T2 - a framework for the analysis of interaction networks in structural ensembles of proteins

AU - Tiberti, Matteo

AU - Invernizzi, Gaetano

AU - Lambrughi, Matteo

AU - Inbar, Yuval

AU - Schreiber, Gideon

AU - Papaleo, Elena

PY - 2014/4/28

Y1 - 2014/4/28

N2 - In the last years, a growing interest has been gathering around the ability of Molecular Dynamics (MD) to provide insight into the paths of long-range structural communication in biomolecules. The knowledge of the mechanisms related to structural communication helps in the rationalization in atomistic details of the effects induced by mutations, ligand binding, and the intrinsic dynamics of proteins. We here present PyInteraph, a tool for the analysis of structural ensembles inspired by graph theory. PyInteraph is a software suite designed to analyze MD and structural ensembles with attention to binary interactions between residues, such as hydrogen bonds, salt bridges, and hydrophobic interactions. PyInteraph also allows the different classes of intra- and intermolecular interactions to be represented, combined or alone, in the form of interaction graphs, along with performing network analysis on the resulting interaction graphs. The program also integrates the network description with a knowledge-based force field to estimate the interaction energies between side chains in the protein. It can be used alone or together with the recently developed xPyder PyMOL plugin through an xPyder-compatible format. The software capabilities and associated protocols are here illustrated by biologically relevant cases of study. The program is available free of charge as Open Source software via the GPL v3 license at http://linux.btbs.unimib.it/pyinteraph/ .

AB - In the last years, a growing interest has been gathering around the ability of Molecular Dynamics (MD) to provide insight into the paths of long-range structural communication in biomolecules. The knowledge of the mechanisms related to structural communication helps in the rationalization in atomistic details of the effects induced by mutations, ligand binding, and the intrinsic dynamics of proteins. We here present PyInteraph, a tool for the analysis of structural ensembles inspired by graph theory. PyInteraph is a software suite designed to analyze MD and structural ensembles with attention to binary interactions between residues, such as hydrogen bonds, salt bridges, and hydrophobic interactions. PyInteraph also allows the different classes of intra- and intermolecular interactions to be represented, combined or alone, in the form of interaction graphs, along with performing network analysis on the resulting interaction graphs. The program also integrates the network description with a knowledge-based force field to estimate the interaction energies between side chains in the protein. It can be used alone or together with the recently developed xPyder PyMOL plugin through an xPyder-compatible format. The software capabilities and associated protocols are here illustrated by biologically relevant cases of study. The program is available free of charge as Open Source software via the GPL v3 license at http://linux.btbs.unimib.it/pyinteraph/ .

U2 - 10.1021/ci400639r

DO - 10.1021/ci400639r

M3 - Journal article

C2 - 24702124

SN - 1549-9596

VL - 54

SP - 1537

EP - 1551

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

IS - 5

ER -