ArticleNucleic acids research2015
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 196 papers.
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Who cites it
196 citing papers in PubMed, 408 citations in OpenAlex.
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- Beyond the flat screen: evaluating virtual reality as a complementary tool for molecular docking in drug discovery.Journal of computer-aided molecular design · 2026Review
- In Silico Structure-Guided Design of Peptide Candidates Targeting γ-Secretase Subunit Assembly.Proteins · 2026Article
- Quantum Pharmacophore-Based Virtual Screening Enables Prospective Discovery of Chemotype-Diverse Dengue NS5 Inhibitors.Journal of chemical information and modeling · 2026Article
- Structural Prediction and Antigenic Characterization of Recombinant Nucleocapsid Protein (p14) of Small Ruminant Lentivirus.Viruses · 2026Article
- Prediction of drug hypersensitivity by comprehensive modeling of HLA-peptidomes.Briefings in bioinformatics · 2026Article
- The chromatin reader ZMYND8 recruits the NuRD component GATAD2A through its MYND domain to regulate MAPT213 long noncoding RNA transcription.The Journal of biological chemistry · 2026Article
- Rational Design of a Novel Anti-Cancer Hybrid Peptide Inhibiting the PI3K/AKT and CDK2 Signaling Pathways using Molecular Dynamics Simulations.Probiotics and antimicrobial proteins · 2026Article
- A human telomerase reverse transcriptase-derived peptide GV1001 rescues neurodegeneration in a mouse model of Alzheimer disease.Experimental & molecular medicine · 2026Article
- From By-Product to Bioactive: New Antioxidant and Bioavailable Peptides Derived from Milk Permeate Targeting the Nrf2/Keap1 Pathway in Intestinal Cell Models.Antioxidants (Basel, Switzerland) · 2026Article
- Peptide-protein docking: from physics-based models to generative intelligence.Chemical communications (Cambridge, England) · 2026Review
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions.Acta pharmacologica Sinica · 2026Article
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Virulence factors ofFrontiers in microbiology · 2026Article
- In silico discovery of umami peptides: From sequence-based intelligent models to structure-function mechanistic insight.Current research in food science · 2026Review
- Recent advances in computational antimicrobial peptide discovery through big data, modeling, and artificial intelligence and their interplay in ushering the next golden era of drug development.Frontiers in bioinformatics · 2026Review
- Lab to codes: multimodel advanced AI-driven pipelines to drive antimicrobial peptide design for the post-antibiotic era.Frontiers in cellular and infection microbiology · 2026Review
136 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock.
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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.