ArticleNucleic acids research2012
PepSite: prediction of peptide-binding sites from protein surfaces.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- Peptide-protein docking: from physics-based models to generative intelligence.Chemical communications (Cambridge, England) · 2026Review
- Bioactive peptides targeting dyslipidemia and atherosclerosis: from computational discovery and data bottlenecks to precision medicine translation.Frontiers in molecular biosciences · 2026Review
- Antihypertensive and antioxidant peptide identification and storage stability assessment of novel probiotic fermented sheep milk: A comparative study with bovine milk.Food chemistry: X · 2025Article
- Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.Journal of chemical information and modeling · 2024Article
- Antihypertensive and Antidiabetic Drug Candidates from Milkfish (Foods (Basel, Switzerland) · 2024Article
- Colorimetric sensing for translational applications: from colorants to mechanisms.Chemical Society reviews · 2024Review
- GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach.Briefings in bioinformatics · 2024Article
- Application of Computational Techniques in Antibody Fc-Fused Molecule Design for Therapeutics.Molecular biotechnology · 2024Review
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- Novel Plant-Protein (Quinoa) Derived Bioactive Peptides with Potential Anti-Hypercholesterolemic Activities: Identification, Characterization and Molecular Docking of Bioactive Peptides.Foods (Basel, Switzerland) · 2023Article
- Identification andFoods (Basel, Switzerland) · 2023Article
- In Silico Prospecting for Novel Bioactive Peptides from Seafoods: A Case Study on Pacific Oyster (Molecules (Basel, Switzerland) · 2023Article
- Multi-Bioactivity of Protein Digests and Peptides from Oat (Molecules (Basel, Switzerland) · 2022Article
- In-Silico Analysis and Antidiabetic Effect of α-Amylase and α-Glucosidase Inhibitory Peptides from Lupin Protein Hydrolysate: Enzyme-Peptide Interaction Study Using Molecular Docking Approach.Foods (Basel, Switzerland) · 2022Article
- A Photoacoustic-Fluorescent Imaging Probe for Proteolytic Gingipains Expressed by Porphyromonas gingivalis.Angewandte Chemie (International ed. in English) · 2022Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- SARS-CoV-2 peptides bind to NKG2D and increase NK cell activity.Cellular immunology · 2022Article
- In Silico Analysis of Peptide Macrocycle -Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Identification and characterization of cholesterol esterase and lipase inhibitory peptides from amaranth protein hydrolysates.Food chemistry: X · 2021Article
- Application of a Combined Peptidomics andCurrent issues in molecular biology · 2021Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Complex biological functions emerge through intricate protein-protein interaction networks. An important class of protein-protein interaction corresponds to peptide-mediated interactions, in which a short peptide stretch from one partner interacts with a large protein surface from the other partner. Protein-peptide interactions are typically of low affinity and involved in regulatory mechanisms, dynamically reshaping protein interaction networks. Due to the relatively small interaction surface, modulation of protein-peptide interactions is feasible and highly attractive for therapeutic purposes. Unfortunately, the number of available 3D structures of protein-peptide interfaces is very limited. For typical cases where a protein-peptide structure of interest is not available, the PepSite web server can be used to predict peptide-binding spots from protein surfaces alone. The PepSite method relies on preferred peptide-binding environments calculated from a set of known protein-peptide 3D structures, combined with distance constraints derived from known peptides. We present an updated version of the web server that is orders of magnitude faster than the original implementation, returning results in seconds instead of minutes or hours. The PepSite web server is available at http://pepsite2.russelllab.org.
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Registered trials
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