ArticleProtein science : a publication of the Protein Society2018
Dockground: A comprehensive data resource for modeling of protein complexes.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- Dockground: Expanding the Resource to Protein-DNA Complexes.Journal of molecular biology · 2026Article
- Article
- MVSO-PPIS: a structured objective learning model for protein-protein interaction sites prediction via multi-view graph information integration.Bioinformatics (Oxford, England) · 2025Article
- Dockground: The Resource Expands to Protein-RNA Interactome.Journal of molecular biology · 2025Article
- Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction.Nature communications · 2025Article
- SpatConv Enables the Accurate Prediction of Protein Binding Sites by a Pretrained Protein Language Model and an Interpretable Bio-spatial Convolution.Research (Washington, D.C.) · 2025Article
- A Survey of Deep Learning Methods and Tools for Protein Binding Site Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks.Computational and structural biotechnology journal · 2025Article
- Pair-EGRET: enhancing the prediction of protein-protein interaction sites through graph attention networks and protein language models.Bioinformatics (Oxford, England) · 2024Article
- Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions.Genomics, proteomics & bioinformatics · 2024Article
- Leveraging machine learning models for peptide-protein interaction prediction.RSC chemical biology · 2024Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Article
- Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.GigaScience · 2024Article
- SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders.Communications biology · 2023Article
- Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics · 2023Article
- Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding.Global challenges (Hoboken, NJ) · 2023Article
- A gated graph transformer for protein complex structure quality assessment and its performance in CASP15.Bioinformatics (Oxford, England) · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
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7 authors.
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Abstract
Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, and developing intermolecular potentials, search procedures, and scoring functions. Development of protein-protein docking techniques requires thorough benchmarking of different parts of the docking protocols on carefully curated sets of protein-protein complexes. We present a comprehensive description of the Dockground resource (http://dockground.compbio.ku.edu) for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2. The resource offers a variety of interconnected datasets of protein-protein complexes and other data for the development and testing of different aspects of protein docking methodologies. Based on protein-protein complexes extracted from the PDB biounit files, Dockground offers sets of X-ray unbound, simulated unbound, model, and docking decoy structures. All datasets are freely available for download, as a whole or selecting specific structures, through a user-friendly interface on one integrated website.
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