ArticlePLoS computational biology2009
Accurate prediction of peptide binding sites on protein surfaces.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 175 citations in OpenAlex.
- Accurate Identification of Protein Binding Sites for All Drug Modalities Using ALLSites.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An ensemble-based model comprising deep learning for predicting peptide-binding residues in proteins.NAR genomics and bioinformatics · 2025Article
- Prediction of Protein-Peptide Binding Sites Using PepBCL.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PepCA: Unveiling protein-peptide interaction sites with a multi-input neural network model.iScience · 2024Article
- Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach.Briefings in bioinformatics · 2024Article
- Leveraging machine learning models for peptide-protein interaction prediction.RSC chemical biology · 2024Review
- A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond.Briefings in bioinformatics · 2024Review
- Article
- DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.Bioinformatics (Oxford, England) · 2023Article
- PepCNN deep learning tool for predicting peptide binding residues in proteins using sequence, structural, and language model features.Scientific reports · 2023Article
- Sequence alterations affect the antidiabetic attributes of hazelnut peptide fractions during the industrial manufacture and simulated digestion of hazelnut paste.Journal of food science and technology · 2023Article
- Review
- A Photoacoustic-Fluorescent Imaging Probe for Proteolytic Gingipains Expressed by Porphyromonas gingivalis.Angewandte Chemie (International ed. in English) · 2022Article
- SARS-CoV-2 peptides bind to NKG2D and increase NK cell activity.Cellular immunology · 2022Article
- Tombul hazelnut (Food chemistry: X · 2021Article
- Improving Docking Power for Short Peptides Using Random Forest.Journal of chemical information and modeling · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Docking Flexible Cyclic Peptides withJournal of chemical theory and computation · 2019Article
- A Comprehensive Review on Current Advances in Peptide Drug Development and Design.International journal of molecular sciences · 2019Review
8 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many important protein-protein interactions are mediated by the binding of a short peptide stretch in one protein to a large globular segment in another. Recent efforts have provided hundreds of examples of new peptides binding to proteins for which a three-dimensional structure is available (either known experimentally or readily modeled) but where no structure of the protein-peptide complex is known. To address this gap, we present an approach that can accurately predict peptide binding sites on protein surfaces. For peptides known to bind a particular protein, the method predicts binding sites with great accuracy, and the specificity of the approach means that it can also be used to predict whether or not a putative or predicted peptide partner will bind. We used known protein-peptide complexes to derive preferences, in the form of spatial position specific scoring matrices, which describe the binding-site environment in globular proteins for each type of amino acid in bound peptides. We then scan the surface of a putative binding protein for sites for each of the amino acids present in a peptide partner and search for combinations of high-scoring amino acid sites that satisfy constraints deduced from the peptide sequence. The method performed well in a benchmark and largely agreed with experimental data mapping binding sites for several recently discovered interactions mediated by peptides, including RG-rich proteins with SMN domains, Epstein-Barr virus LMP1 with TRADD domains, DBC1 with Sir2, and the Ago hook with Argonaute PIWI domain. The method, and associated statistics, is an excellent tool for predicting and studying binding sites for newly discovered peptides mediating critical events in biology.
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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.