ArticleBioinformatics (Oxford, England)2017
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Impact of M and E protein mutations in SARS-CoV-2 Omicron variants on reduced antibody binding and increased structural stability: a bioinformatics study (2021-2023).BMC genomics · 2026Article
- Structure-Guided Design of an Interface-Derived Inhibitor Peptide Against Spodoptera frugiperda Digestive Trypsins.Archives of insect biochemistry and physiology · 2026Article
- Dihydro-R demonstrates innate immunity against Adenovirus-7 by suppressing the NF-κB/JAK-STAT pathway in a SIRT1-dependent manner.Biochemistry and biophysics reports · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- Semaglutide Mitigates Ischemic Brain Injury by Inhibiting Ferroptosis via Modulation of FoXO1 and DRP1 Pathways.Molecular neurobiology · 2025Article
- DiffPepDock: Efficient protein-peptide docking and binder screening via SE(3)-equivariant diffusion.Protein science : a publication of the Protein Society · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach.Journal, genetic engineering & biotechnology · 2025Article
- Co-Localized in Amyloid Plaques Cathepsin B as a Source of Peptide Analogs Potential Drug Candidates for Alzheimer's Disease.Biomolecules · 2024Article
- Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus.Computational and structural biotechnology journal · 2024Article
- Multiple allostery in the regulation of PDGFR beta kinase activities.Acta biochimica et biophysica Sinica · 2024Article
- Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives.Amino acids · 2024Review
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- Development of multi epitope subunit vaccines against emerging carp viruses Cyprinid herpesvirus 1 and 3 using immunoinformatics approach.Scientific reports · 2024Article
- Simulation and Computational Study of RING Domain Mutants of BRCA1 and Ube2k in AD/PD Pathophysiology.Molecular biotechnology · 2024Article
- Interaction of Tau with G-Protein-Coupled Purinergic P2Y12 Receptor by Molecular Docking and Molecular Dynamic Simulation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Molecular Dynamics Simulations in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques.Current topics in medicinal chemistry · 2024Review
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5 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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Abstract
summaryWe present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions. AVAILABILITY AND IMPLEMENTATION: The method is available as part of the protein-protein docking server ClusPro at https://peptidock.cluspro.org/nousername.php. CONTACT: midas@laufercenter.org or oraf@ekmd.huji.ac.il. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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