ArticlePloS one2015
VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- A comprehensive survey of scoring functions for protein docking models.BMC bioinformatics · 2025Article
- Computational prediction of multiple antigen epitopes.Bioinformatics (Oxford, England) · 2024Article
- Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity inNAR genomics and bioinformatics · 2024Article
- Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation.iScience · 2024Article
- Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures.Methods in molecular biology (Clifton, N.J.) · 2022Review
- SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions.BMC bioinformatics · 2021Article
- Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions.Protein science : a publication of the Protein Society · 2020Article
- Coarse-grained (hybrid) integrative modeling of biomolecular interactions.Computational and structural biotechnology journal · 2020Review
- BIPSPI: a method for the prediction of partner-specific protein-protein interfaces.Bioinformatics (Oxford, England) · 2019Article
- On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.Bioinformatics (Oxford, England) · 2018Article
- 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.Biophysical journal · 2016Article
- Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.Biophysical journal · 2016Article
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5 authors.
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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 users to browser and visualize V-D2OCK predictions from the convenience of their web-browsers.
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