ArticleNucleic acids research2010
PepX: a structural database of non-redundant protein-peptide complexes.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Context-dependent peptide recognition shapes tyrosine kinase substrate specificity beyond consensus motifs.bioRxiv : the preprint server for biology · 2026Article
- DiffPepDock: Efficient protein-peptide docking and binder screening via SE(3)-equivariant diffusion.Protein science : a publication of the Protein Society · 2025Article
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.Current medicinal chemistry · 2024Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm.BMC bioinformatics · 2021Article
- DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands.Database : the journal of biological databases and curation · 2020Article
- PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.Journal of computational chemistry · 2020Article
- ProtCID: a data resource for structural information on protein interactions.Nature communications · 2020Article
- Article
- A Comprehensive Review on Current Advances in Peptide Drug Development and Design.International journal of molecular sciences · 2019Review
- Building Bridges Between Structural and Network-Based Systems Biology.Molecular biotechnology · 2019Review
- Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations.Frontiers in molecular biosciences · 2019Article
- FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1).Nucleic acids research · 2018Article
- Computer-aided design of amino acid-based therapeutics: a review.Drug design, development and therapy · 2018Review
- PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode.Protein science : a publication of the Protein Society · 2018Article
- Protein structural motifs in prediction and design.Current opinion in structural biology · 2017Review
- A Comprehensive View of the β-Arrestinome.Frontiers in endocrinology · 2017Article
- PepComposer: computational design of peptides binding to a given protein surface.Nucleic acids research · 2016Article
- DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.Database : the journal of biological databases and curation · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although protein-peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. Peptide-mediated interactions are a prime target for drug design because they are predominantly present in signaling and regulatory networks. A reliable data set of nonredundant protein-peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein-peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. The final data set contains 505 unique protein-peptide interface clusters from 1431 complexes. Thorough annotation of each complex with both biological and structural information facilitates searching for and browsing through individual complexes and clusters. Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database.
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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.