VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy

PloS One
Joan SeguraNarcis Fernandez-Fuentes

Abstract

The experimental determination of the structure of protein complexes cannot keep pace with the generation of interactomic data, hence resulting in an ever-expanding gap. As the structural details of protein complexes are central to a full understanding of the function and dynamics of the cell machinery, alternative strategies are needed to circumvent the bottleneck in structure determination. Computational protein docking is a valid and valuable approach to model the structure of protein complexes. In this work, we describe a novel computational strategy to predict the structure of protein complexes based on data-driven docking: VORFFIP-driven dock (V-D2OCK). This new approach makes use of our newly described method to predict functional sites in protein structures, VORFFIP, to define the region to be sampled during docking and structural clustering to reduce the number of models to be examined by users. V-D2OCK has been benchmarked using a validated and diverse set of protein complexes and compared to a state-of-art docking method. The speed and accuracy compared to contemporary tools justifies the potential use of VD2OCK for high-throughput, genome-wide, protein docking. Finally, we have developed a web interface that allows ...Continue Reading

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Citations

Feb 6, 2016·Biophysical Journal·Sjoerd J de VriesMartin Zacharias
Jan 17, 2016·Biophysical Journal·Joan SeguraJose Maria Carazo
Nov 21, 2016·Current Opinion in Structural Biology·M Michael GromihaSherlyn Jemimah
Oct 14, 2017·Bioinformatics·Manuel Alejandro Marín-LópezBaldo Oliva
Jul 19, 2018·Bioinformatics·Ruben Sanchez-GarciaJoan Segura
Feb 27, 2020·Current Topics in Medicinal Chemistry·Olivia SlaterMaria Kontoyianni
Jun 18, 2016·Journal of Enzyme Inhibition and Medicinal Chemistry·Giulio PoliTiziano Tuccinardi
Jun 11, 2016·Biochemical Society Transactions·Daniel PoglayenNarcis Fernandez-Fuentes
Aug 17, 2020·Protein Science : a Publication of the Protein Society·Alberto MeseguerBaldo Oliva
Jun 10, 2020·Computational and Structural Biotechnology Journal·Jorge Roel-Touris, Alexandre M J J Bonvin
Sep 26, 2020·Journal of Molecular Biology·Patricia Mirela-BotaNarcis Fernandez-Fuentes

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Software Mentioned

ZDOCK
VORFFIP
ES3DC
PATCH
GROMACS
D 2 OCK
CAPRI
DIMPLOT
D OCK
ZRANK

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