UMMS Affiliation

Program in Bioinformatics and Integrative Biology

Date

2-14-2017

Document Type

Article

Disciplines

Biochemistry | Bioinformatics | Biophysics | Computational Biology | Structural Biology

Abstract

Motivation: In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction.

Results: Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100.

Availability and Implementation: IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/ approximately SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request.

Contact: moal@ebi.ac.uk.

Supplementary information: Supplementary data are available at Bioinformatics online.

Rights and Permissions

© The Author 2017. Citation: Bioinformatics (2017) 33 (12): 1806-1813. doi: 10.1093/bioinformatics/btx068. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Keywords

IRaPPA, protein structure, information retrieval

PubMed ID

28200016

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

 
 

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