ProteinFishing: A protein complex generator within the ModelX toolsuite.

SUMMARY: Accurate three-dimensional modelling of protein-protein interactions (PPI) is essential to compensate for the absence of experimentally-determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2/interleukin-10 structural models in agreement with experimental data. IMPLEMENTATION AND DEPENDENCIES: ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C ++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit, and Windows-32bit operating systems. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.