ArticleBriefings in bioinformatics2019
Protein-peptide docking using CABS-dock and contact information.
Article in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Structural Prediction and Antigenic Characterization of Recombinant Nucleocapsid Protein (p14) of Small Ruminant Lentivirus.Viruses · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.Journal of chemical theory and computation · 2025Article
- Accumulation of TDP-43 causes karyopherin-α4 pathology that characterises amyotrophic lateral sclerosis.Frontiers in neuroscience · 2025Article
- In Silico Strategies to Predict Anti-aging Features of Whey Peptides.Molecular biotechnology · 2024Article
- How the immune response to the structural proteins of SARS-CoV-2 affects the retinal vascular endothelial cells: an immune thrombotic and/or endotheliopathy process with in silico modeling.Immunologic research · 2024Article
- Structure prediction of linear and cyclic peptides using CABS-flex.Briefings in bioinformatics · 2024Article
- A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.Current medicinal chemistry · 2024Article
- In Silico Design of a New Epitope-Based Vaccine against Grass Group 1 Allergens.Advances in respiratory medicine · 2023Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- A novel anti-membrane CD30 single-chain variable fragment discovered from the human phage library: A potential targeted immunotherapy.PloS one · 2023Article
- Harnessing protein folding neural networks for peptide-protein docking.Nature communications · 2022Article
- Article
- Identification of a peptide binding to cancer antigen Kita-kyushu lung cancer antigen 1 from a phage-display library.Cancer science · 2021Article
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Molecular Dynamics Scoring of Protein-Peptide Models Derived from Coarse-Grained Docking.Molecules (Basel, Switzerland) · 2021Article
- Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.Briefings in bioinformatics · 2021Article
- Article
- Molecular Functionality of Plant Proteins from Low- to High-Solid Systems with Ligand and Co-Solute.International journal of molecular sciences · 2020Review
- Flexible docking of peptides to proteins using CABS-dock.Protein science : a publication of the Protein Society · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CABS-dock is a computational method for protein-peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein-peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and randomly chosen native protein-peptide contact to validate the protocol on the peptiDB benchmark. The contact information significantly improved CABS-dock performance. The protocol has been made available as a new feature of the CABS-dock web server (at http://biocomp.chem.uw.edu.pl/CABSdock/). SHORT ABSTRACT: CABS-dock is a tool for flexible docking of peptides to proteins. In this article, we present a protocol for CABS-dock docking driven by information about protein-peptide contact(s). Using information on individual protein-peptide contacts allows to improve the accuracy of CABS-dock docking.
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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.