ArticleJournal of chemical information and modeling2025
HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
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- Combining AI Structure Prediction and Integrative Modeling for Nanobody-Antigen Complexes.Journal of chemical information and modeling · 2026Article
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- ABAG-Rank: improving model selection of AlphaFold antibody-antigen complexes by learning to rank.Bioinformatics (Oxford, England) · 2026Article
- EscaPRRS-ORF5: a structure-aware evolutionary framework for prioritizing immune escape-prone variants in porcine reproductive and respiratory syndrome virus.Bioinformatics (Oxford, England) · 2026Article
- A Multi-Model Strategy for Optimizing Hepatitis B Virus preS1 Epitope Recognition by the Antibody HzKR127.Current issues in molecular biology · 2026Article
- FUCA2 Sustains AKT Signaling and Suppresses Senescence by Antagonizing FUT3-Mediated ErbB3 Fucosylation in Lung Adenocarcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ProteinDock: A physics-informed layer to improve protein-protein docking reliability.bioRxiv : the preprint server for biology · 2026Article
- A Multi-Engine Consensus Docking Pipeline for RNA Aptamer Screening Against ACC Oxidase (ACO): Statistical Validation, Machine Learning Analysis, and Pilot Cross-Target Evaluation Against ACC Synthase (ACS).International journal of molecular sciences · 2026Article
- DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.Communications biology · 2026Article
- SwiftTCR: efficient computational docking protocol of TCRpMHC-I complexes using restricted rotation matrices.Briefings in bioinformatics · 2026Article
- FRZB-induced anti-angiogenic effect via Caveolin-1-mediated TGFβ signalling.Nature communications · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Mirror Effect of Parvalbumin and Connexin 43 Expression in the Acute and Subacute Phases After Penetrating Traumatic Brain Injury Reveals a Non-Canonical Interaction.Molecules (Basel, Switzerland) · 2026Article
- Biosensor-Based Detection of Calprotectin and Lactoferrin as Neutrophil-Derived Markers of Inflammatory Bowel Diseases: From Molecular Pathophysiology to Point-of-Care Platforms.International journal of molecular sciences · 2026Review
- Discovery and characterization of an anti-Frontiers in microbiology · 2026Article
- Seq2Bind webserver for binding site prediction from sequences using fine-tuned protein language models.NAR genomics and bioinformatics · 2025Article
- PTF-Vāc: An explainable and generative deep co-learning encoder-decoder system for ab initio discovery of plant transcription factor binding sites.Plant communications · 2025Article
- A Comprehensive Overview of Antimicrobial Peptides: Broad-Spectrum Activity, Computational Approaches, and Applications.Antibiotics (Basel, Switzerland) · 2025Review
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HADDOCK is a widely used resource for integrative modeling of a variety of biomolecular complexes that is able to incorporate experimental knowledge into physics-based calculations during complex prediction, refinement, scoring and analysis. Here we introduce HADDOCK3, the new modular version of the program, in which the original, parametrizable albeit rigid pipeline has been first broken down into a catalogue of independent modules and then enriched with powerful analysis tools and third-party integrations. Thanks to this increased flexibility, HADDOCK3 can now handle multiple integrative modeling scenarios, providing a valuable, physics-based tool to enrich and complement the predictions made by machine learning algorithms in the post-AlphaFold era. We present examples of successful applications of HADDOCK3 that were not feasible with the previous versions of HADDOCK, highlighting its expanded capabilities. The HADDOCK3 software source code is freely available from the GitHub repository (https://github.com/haddocking/haddock3) and comes with an online user guide (www.bonvinlab.org/haddock3-user-manual). All example data described in this manuscript are available at https://github.com/haddocking/haddock3-paper-data.
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Registered trials
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.