ArticleBioinformatics (Oxford, England)2024
DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Article
- HDX-MS-Guided computational modeling for rapid and accurate antibody-antigen interface mapping.mAbs · 2026Article
- Evaluating AlphaFold Tools and Related Scoring Functions for Protein-peptide Complex Prediction.Genomics, proteomics & bioinformatics · 2026Article
- Evaluation of methods for AlphaFold-based integrative modeling.bioRxiv : the preprint server for biology · 2026Article
- Dockground: Expanding the Resource to Protein-DNA Complexes.Journal of molecular biology · 2026Article
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- Limits of deep-learning-based RNA prediction methods.Nucleic acids research · 2026Article
- From Ternary Modeling to Predictive PROTAC Design: A Computational Perspective.Journal of chemical information and modeling · 2026Article
- Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.Journal of chemical information and modeling · 2026Article
- COMPASS: A Computational Pipeline to Identify Linkers Predicting Ubiquitinable PROTAC-Induced Ternary Complexes.ChemMedChem · 2026Article
- ProteinDock: A physics-informed layer to improve protein-protein docking reliability.bioRxiv : the preprint server for biology · 2026Article
- Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase.bioRxiv : the preprint server for biology · 2026Article
- A comparative and exploratory analysis of computational methods for TCR structural prediction and antigen-specific TCR discovery.Briefings in bioinformatics · 2026Article
- Incorporating Surfaced-Induced Dissociation Mass Spectrometry Data into an AlphaFold-derived deep learning network improves protein structure prediction.bioRxiv : the preprint server for biology · 2026Article
- A Chromatin Biology Assessment of AlphaFold3.bioRxiv : the preprint server for biology · 2026Article
- Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families.BioData mining · 2026Review
- Integrative Computational Prediction Strategy for Antibody-Antigen Binding: A Case Study on Interleukin-1 Beta.Journal of chemical information and modeling · 2026Article
- NuConf: a rotamer library for DNA and RNA and its implementation in the protein design software MUMBO.Scientific reports · 2026Article
- Evaluating deep learning based structure prediction methods on antibody-antigen complexes.Bioinformatics (Oxford, England) · 2026Article
- Atlas of predicted protein complex structures across kingdoms.Nature communications · 2026Article
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2 authors.
Funding
Abstract
motivationIt is important to assess the quality of modeled biomolecules to benchmark and assess the performance of different prediction methods. DockQ has emerged as the standard tool for assessing the quality of protein interfaces in model structures against given references. However, as predictions of large multimers with multiple chains become more common, DockQ needs to be updated with more functionality for robustness and speed. Moreover, as the field progresses and more methods are released to predict interactions between proteins and other types of molecules, such as nucleic acids and small molecules, it becomes necessary to have a tool that can assess all types of interactions.
resultsHere, we present a complete reimplementation of DockQ in pure Python. The updated version of DockQ is more portable, faster and introduces novel functionalities, such as automatic DockQ calculations for multiple interfaces and automatic chain mapping with multi-threading. These enhancements are designed to facilitate comparative analyses of protein complexes, particularly large multi-chain complexes. Furthermore, DockQ is now also able to score interfaces between proteins, nucleic acids, and small molecules. AVAILABILITY AND IMPLEMENTATION: DockQ v2 is available online at: https://wallnerlab.org/DockQ.
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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.