ArticleProtein and peptide letters2014
MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.
Article in Protein and peptide letters, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- The immune protection of OMP16-specific IgM against Brucella infection.BMC biology · 2026Article
- Interactomics: Dissecting Protein Networks in Living Systems.Advances in experimental medicine and biology · 2026Review
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
- Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach.International journal of molecular sciences · 2025Article
- Importance of Computer-aided Drug Design in Modern Pharmaceutical Research.Current drug discovery technologies · 2025Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Docking Foundations: From Rigid to Flexible Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mapping the protein-protein interactome in the tumor immune microenvironment.Antibody therapeutics · 2023Review
- MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory.BMC research notes · 2023Article
- Recent developments of sequence-based prediction of protein-protein interactions.Biophysical reviews · 2022Review
- Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions.BMC bioinformatics · 2022Article
- Protein-protein interaction prediction with deep learning: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain.International journal of molecular sciences · 2021Review
- Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction.Current genomics · 2020Review
- Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces.Biophysics and physicobiology · 2020Article
- Article
- DISPOT: a simple knowledge-based protein domain interaction statistical potential.Bioinformatics (Oxford, England) · 2019Article
- Computational identification of protein-protein interactions in model plant proteomes.Scientific reports · 2019Article
- Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus.Evolutionary bioinformatics online · 2019Article
- An integration of deep learning with feature embedding for protein-protein interaction prediction.PeerJ · 2019Article
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5 authors.
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Abstract
The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have been investigating a protein docking approach based on shape complementarity and physicochemical properties. We describe here the development of the protein-protein docking software package "MEGADOCK" that samples an extremely large number of protein dockings at high speed. MEGADOCK reduces the calculation time required for docking by using several techniques such as a novel scoring function called the real Pairwise Shape Complementarity (rPSC) score. We showed that MEGADOCK is capable of exhaustive PPI screening by completing docking calculations 7.5 times faster than the conventional docking software, ZDOCK, while maintaining an acceptable level of accuracy. When MEGADOCK was applied to a subset of a general benchmark dataset to predict 120 relevant interacting pairs from 120 x 120 = 14,400 combinations of proteins, an F-measure value of 0.231 was obtained. Further, we showed that MEGADOCK can be applied to a large-scale protein-protein interaction-screening problem with accuracy better than random. When our approach is combined with parallel high-performance computing systems, it is now feasible to search and analyze protein-protein interactions while taking into account three-dimensional structures at the interactome scale. MEGADOCK is freely available at http://www.bi.cs.titech.ac.jp/megadock.
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