ReviewNature protocols2024
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 301 papers.
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Who cites it
301 citing papers in PubMed.
- The regulation of AsfR on tmRNA expression mediates bacterial motility and virulence inVirulence · 2026Article
- Article
- Identification of the first peptide inhibitor of UBE2C enzymatic activity: insights from metadynamics-guided folding and binding studies.Journal of enzyme inhibition and medicinal chemistry · 2026Article
- Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55.Proteins · 2026Article
- Small-molecule activators of theiScience · 2026Article
- Characterization of Full-Length Antibody Complexes Through HDX-Mass Spectrometry Coupled With NMR Spectroscopy: New Insight Into Avelumab/PD-L1 Interaction.Angewandte Chemie (International ed. in English) · 2026Article
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- Molecular mechanism of complement interference by Streptococcus pyogenes nuclease A.Communications biology · 2026Article
- An iron-regulated methionine redox axis governs adipose browning and cancer cachexia.Nature cancer · 2026Article
- Integrated multi-omics identifies lineage-dependent myeloid cells recruitment and the APP-CD74 axis as an immunoregulatory target in pediatric high-grade glioma.Acta neuropathologica · 2026Article
- Upstream regulatory mechanisms and clinical significance of IQGAP2 deficiency in affecting PI3K activity to drive cell proliferation.Human cell · 2026Article
- Comparative Genomics-Guided Epitope Prioritization and in Silico Design of a Multi-Epitope DNA Vaccine Candidate Against Megalocytivirus pagrus 1.Marine biotechnology (New York, N.Y.) · 2026Article
- Peptides adopt stable omega-loop structures in concentrated sulfuric acid.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- CircLAMA5 traps Sam68 in the cytoplasm to regulate alternative splicing and drive sunitinib resistance in ccRCC.Oncogene · 2026Article
- Sodium Channel Blockers Demonstrate Binding Affinity for the Tandem Tudor Domain of the Epigenetic Hub UHRF1.ChemMedChem · 2026Article
- Leveraging high-throughput proteomics and AI-based protein folding to accelerate VAV1 molecular glue discovery.Nature communications · 2026Article
- Multiomics approaches reveal direct NF-κB p65 target genes in pancreatic islets during cytokine exposure and in type 1 diabetes.American journal of physiology. Endocrinology and metabolism · 2026Article
- Gut Microbiota-Elicited Aberrant Phosphorylation Induces Protein Structural Anomalies: A Non-Negligible Pathogenic Driver of Autism Spectrum Disorder.Microorganisms · 2026Article
- Contact Occupancy and Per-Residue Energetic Contributions Distinguish Aflatoxin B1 Nanobodies with Different Binding Affinities.Biomolecules · 2026Article
- Syntaxin-3 Regulates Tight Junction Assembly in Human Retinal Pigment Epithelium.Cell biochemistry and function · 2026Article
241 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
Abstract
Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the information required to fully model biomolecular complexes at atomic resolution, particularly for large and heterogeneous assemblies. Integrative computational approaches have, therefore, gained popularity, complementing traditional experimental methods in structural biology. Here, we introduce HADDOCK2.4, an integrative modeling platform, and its updated web interface ( https://wenmr.science.uu.nl/haddock2.4 ). The platform seamlessly integrates diverse experimental and theoretical data to generate high-quality models of macromolecular complexes. The user-friendly web server offers automated parameter settings, access to distributed computing resources, and pre- and post-processing steps that enhance the user experience. To present the web server's various interfaces and features, we demonstrate two different applications: (i) we predict the structure of an antibody-antigen complex by using NMR data for the antigen and knowledge of the hypervariable loops for the antibody, and (ii) we perform coarse-grained modeling of PRC1 with a nucleosome particle guided by mutagenesis and functional data. The described protocols require some basic familiarity with molecular modeling and the Linux command shell. This new version of our widely used HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types.
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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.