pyScoMotif: Discovery of similar 3D structural motifs across proteins

Abstract

MotivationThe fast and accurate detection of similar geometrical arrangements of protein residues, known as 3-dimensional (3D) structural motifs, is highly relevant for many applications such as binding region and catalytic site detection, drug discovery and structure conservation analyses. With the recent publication of new protein structure prediction methods, the number of available protein structures is exploding, which makes efficient and easy-to-use tools for identifying 3D structural motifs essential.ResultsWe present an open-source Python package that enables the search for both exact and mutated motifs with position-specific residue substitutions. The tool is fast, accurate and suitable to run both on computer clusters and personal laptops. Successful application of pyScoMotif to catalytic site identification is showcased.AvailabilityThe pyScoMotif package can be installed from the PyPI repository and is also available athttps://github.com/3BioCompBio/pyScoMotif. It is free to use for non-commercial purposes; for commercial purposes, please contact us.