ArticleNucleic acids research2014
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
42 citing papers in PubMed, 93 citations in OpenAlex.
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- Achieving protease substrate-specific inhibition by mAb dual functional selections.Protein science : a publication of the Protein Society · 2026Article
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- Application of Phage-Displayed Peptide Library for Epitope Mapping.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Bioactive peptides targeting dyslipidemia and atherosclerosis: from computational discovery and data bottlenecks to precision medicine translation.Frontiers in molecular biosciences · 2026Review
- Identification and characterization of a Fibrillin-1 derived matrikine for cardiac regeneration and repair.bioRxiv : the preprint server for biology · 2025Article
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Natural L-Hexapeptides with Therapeutic Potential for Alzheimer's Disease and Tauopathies.ACS omega · 2025Article
- The antimicrobial peptide Angie 5 inhibits TcdA and TcdB from Clostridioides difficile.Cellular and molecular life sciences : CMLS · 2025Article
- Circular RNA-Encoded Proteins in Disease Pathogenesis.International journal of biological sciences · 2025Review
- PepCA: Unveiling protein-peptide interaction sites with a multi-input neural network model.iScience · 2024Article
- CircSP3 encodes SP3-461aa to promote ccRCC progression via stabilizing MYH9 and activating the PI3K-Akt signaling pathway.Journal of Cancer · 2024Article
- Interaction with the carboxy-terminal tip of SSB is critical for RecG function in E. coli.Nucleic acids research · 2023Article
- Machine learning assessment of the binding region as a tool for more efficient computational receptor-ligand docking.Journal of molecular liquids · 2022Article
- circ-EIF6 encodes EIF6-224aa to promote TNBC progression via stabilizing MYH9 and activating the Wnt/beta-catenin pathway.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Receptor-binding domain-anchored peptides block binding of severe acute respiratory syndrome coronavirus 2 spike proteins with cell surface angiotensin-converting enzyme 2.Frontiers in microbiology · 2022Article
- Peptides Affecting the Outer Membrane Lipid Asymmetry System (MlaA-OmpC/F) Reduce Avian Pathogenic Escherichia coli (APEC) Colonization in Chickens.Applied and environmental microbiology · 2021Article
- Convergent chemoenzymatic synthesis and biological evaluation of a heparan sulfate proteoglycan syndecan-1 mimetic.Chemical communications (Cambridge, England) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder.
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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.