4100245

Residue-interaction from physical adjacency (RIPA): A python package for analyzing protein functions

Date
August 18, 2024

Understanding protein functions through biomodeling is vital towards optimizing properties for various applications. Such instances include screening ligands rapidly to select appropriate candidates for binding, detecting persistent interactions between residues for mutagenesis, and pinpointing key interactions between macromolecules. These challenges can be examined by molecular dynamics (MD) simulations. While present-day software provides analysis over the interactions within the structures of the protein or protein-ligand complex, many are limited to analyzing a single structural snapshot. This may give an initial insight to how the protein interacts with itself, but the persistence of the interactions is difficult to be interpreted. The solution is RIPA (residue interaction from physical adjacency): a Python package utilizing Pteros, a C++ library for analyzing molecular dynamics trajectories, and igraph, a Python library for displaying network graphs. This tool analyzes the interactions based on physical adjacency among protein residues (including ligands) from MD simulations. The RIPA package transforms distance matrices to adjacency matrices for network analysis, and can generate weighted graphs from MD trajectories, display residue interaction network dynamics, and create bipartisan graphs for specified atom groups. Using a C++ based engine for processing MD trajectories, faster speeds are achieved compared to existing pure-Python packages, and scale well with the MD trajectories, both spatially and/or temporally. RIPA is used to display the diverse interaction networks in single proteins, protein-ligand and protein-DNA complexes. The use of igraph provides clean and adjustable graphics for quick visualization or in publication quality.

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