ProteinFishing: a protein complex generator within the ModelX toolsuite

Cianferoni, Damiano; Radusky, Leandro; Head, Sarah A.; Serrano Pubull, Luis, 1982-; Delgado Blanco, Javier

doi:http://dx.doi.org/10.1093/bioinformatics/btaa533

ProteinFishing: a protein complex generator within the ModelX toolsuite

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Citation

Cianferoni D, Radusky LR, Head SA, Serrano L, Delgado, J. ProteinFishing: a protein complex generator within the ModelX toolsuite. Bioinformatics. 2020 Aug 15; 36(14): 4208-4210. DOI: 10.1093/bioinformatics/btaa533

Abstract

Summary: Accurate 3D 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. Availability and implementation: 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. This software is a proprietary license and is distributed as an executable with its correspondent database dumps. It can be downloaded publicly at http://modelx.crg.es/. Licenses are freely available for academic users after registration on the website and are available under commercial license for for-profit organizations or companies.