ProteinFishing: A protein complex generator within the ModelX toolsuite

Damiano Cianferoni, Leandro G Radusky, Sarah A Head, Luis Serrano, Javier Delgado, Arne Elofsson
2020 Bioinformatics  
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
more » ... 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.
doi:10.1093/bioinformatics/btaa533 pmid:32437555 pmcid:PMC7390992 fatcat:xv4p2dyhwnethb5ko3cwtr4oue