ProteinFishing: a protein complex generator within the ModelX toolsuite
Mostra el registre complet Registre parcial de l'ítem
- dc.contributor.author Cianferoni, Damiano
- dc.contributor.author Radusky, Leandro
- dc.contributor.author Head, Sarah A.
- dc.contributor.author Serrano Pubull, Luis, 1982-
- dc.contributor.author Delgado Blanco, Javier
- dc.date.accessioned 2020-10-08T06:20:56Z
- dc.date.available 2020-10-08T06:20:56Z
- dc.date.issued 2020
- dc.description.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.
- dc.description.sponsorship This work was supported by funding from the Spanish Ministry of Science and Innovation (Plan Nacional BFU2015-63571-P). The authors also acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the Centres de Recerca de Catalunya (CERCA) Programme/Generalitat de Catalunya. The project that gave rise to these results was supported by a fellowship from ‘la Caixa’ Foundation (ID 100010434; fellowship code LCF/BQ/DI19/11730061)
- dc.format.mimetype application/pdf
- dc.identifier.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
- dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btaa533
- dc.identifier.issn 1367-4803
- dc.identifier.uri http://hdl.handle.net/10230/45426
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Bioinformatics. 2020 Aug 15;36(14):4208-10
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-63571-P
- dc.rights © 2020 Damiano Cianferoni et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/),which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.subject.other Proteïnes
- dc.subject.other Programació (Ordinadors)
- dc.title ProteinFishing: a protein complex generator within the ModelX toolsuite
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion