ArticleBioinformatics (Oxford, England)2019
CABS-dock standalone: a toolbox for flexible protein-peptide docking.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 92 citations in OpenAlex.
- A peptide-induced regression of low-grade malignant breast tumor via activation of autophagy in breast cancer cells.Molecular medicine (Cambridge, Mass.) · 2026Article
- Discovery of an Endonuclease G-inhibitory Ku80-peptide protecting against leukemogenic rearrangements at the MLL breakpoint cluster.Nature communications · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- Peptide-based drug design using generative AI.Chemical communications (Cambridge, England) · 2026Review
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- A triple-action PROTAC for wild-type p53 cancer therapy.Cell reports. Medicine · 2025Article
- Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.Journal of chemical theory and computation · 2025Article
- The HER2 target for designing novel multi-peptide vaccine against breast cancer using immunoinformatics and molecular dynamic simulation.Biochemistry and biophysics reports · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- The identification of a SARs-CoV2 S2 protein derived peptide with super-antigen-like stimulatory properties on T-cells.Communications biology · 2025Article
- Mechanistic insights into Alpha-Synuclein binding to P2RX7: A molecular dynamic and docking study.PloS one · 2025Article
- Development of a multi-neoepitope vaccine targeting non-small cell lung cancer through reverse vaccinology and bioinformatics approaches.Frontiers in immunology · 2025Article
- Evaluation of predictions of disordered binding regions in the CAID2 experiment.Computational and structural biotechnology journal · 2025Review
- Dissecting the neuroprotective interaction between the BH4 domain of BCL-w and the IP3 receptor.Cell chemical biology · 2024Article
- AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides.Database : the journal of biological databases and curation · 2024Article
- Novel Methodology for the Design of Personalized Cancer Vaccine Targeting Neoantigens: Application to Pancreatic Ductal Adenocarcinoma.Diseases (Basel, Switzerland) · 2024Article
- LiF-MS+, a revised technique for mapping peptide-protein interactions.bioRxiv : the preprint server for biology · 2024Article
- Prediction of virus-host interactions and identification of hot spot residues of DENV-2 and SH3 domain interactions.Archives of microbiology · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryCABS-dock standalone is a multiplatform Python package for protein-peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein-peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation-it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results. AVAILABILITY AND IMPLEMENTATION: CABS-dock standalone is distributed under the MIT licence, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use and installation instructions for Linux, macOS and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/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.