Apr 28, 2020

A C++ library for protein sub-structure search

BioRxiv : the Preprint Server for Biology
J. Zhou, Gevorg Grigoryan


MASTER is a previously published algorithm for protein sub-structure search. Given a database of protein structures and a query structural motif, composed of multiple disjoint segments, it finds all sub-structures from the database that align onto the query to within a pre-specified backbone root-mean-square deviation. Here, we present an improved version of the algorithm, MASTER v.2, in the form of an open-source C++ Application Program Interface library, thereby providing programmatic access to structure search functionality. An entirely reorganized approach to database representation now enables large structural databases to be stored in memory, further simplifying development of automated search-based methods. Given the in-creasingly important role of structure-based data mining, our improved implementation should find ample uses in structural biology applications.

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