ArticleBioinformatics (Oxford, England)2020
Protein docking model evaluation by 3D deep convolutional neural networks.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Evaluating AlphaFold Tools and Related Scoring Functions for Protein-peptide Complex Prediction.Genomics, proteomics & bioinformatics · 2026Article
- TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction.Acta pharmacologica Sinica · 2026Article
- Large Language Models Meet Gynecologic Ultrasound: Advancing the Characterization of ADNEXal Masses.Journal of imaging · 2026Article
- DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.Communications biology · 2026Article
- Article
- AI-Driven De Novo Binder Design: From Structure Prediction to Closed-Loop Optimization.Computational and structural biotechnology journal · 2026Review
- Using AlphaFold and Symmetrical Docking to Predict Protein-Protein Interactions for Exploring Potential Crystallization Conditions.Proteins · 2025Article
- Global profiling of protein complex dynamics with an experimental library of protein interaction markers.Nature biotechnology · 2025Article
- A new age in structural S-layer biology: Experimental and in silico milestones.The Journal of biological chemistry · 2025Review
- Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues.Journal of chemical information and modeling · 2025Article
- Unveiling the new chapter in nanobody engineering: advances in traditional construction and AI-driven optimization.Journal of nanobiotechnology · 2025Review
- A comprehensive survey of scoring functions for protein docking models.BMC bioinformatics · 2025Article
- EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks.Computational and structural biotechnology journal · 2025Article
- EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces.Bioinformatics (Oxford, England) · 2024Article
- ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models.Biomolecules · 2024Review
- MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery.Nature computational science · 2024Article
- ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations.Journal of chemical information and modeling · 2024Article
- DeepRank-GNN-esm: a graph neural network for scoring protein-protein models using protein language model.Bioinformatics advances · 2024Article
- Machine Learning Methods in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
motivationMany important cellular processes involve physical interactions of proteins. Therefore, determining protein quaternary structures provide critical insights for understanding molecular mechanisms of functions of the complexes. To complement experimental methods, many computational methods have been developed to predict structures of protein complexes. One of the challenges in computational protein complex structure prediction is to identify near-native models from a large pool of generated models.
resultsWe developed a convolutional deep neural network-based approach named DOcking decoy selection with Voxel-based deep neural nEtwork (DOVE) for evaluating protein docking models. To evaluate a protein docking model, DOVE scans the protein-protein interface of the model with a 3D voxel and considers atomic interaction types and their energetic contributions as input features applied to the neural network. The deep learning models were trained and validated on docking models available in the ZDock and DockGround databases. Among the different combinations of features tested, almost all outperformed existing scoring functions. AVAILABILITY AND IMPLEMENTATION: Codes available at http://github.com/kiharalab/DOVE, http://kiharalab.org/dove/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.