ArticleJournal of computational chemistry2020
PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.International journal of molecular sciences · 2026Article
- High-throughput discovery of inhibitory protein fragments with AlphaFold.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- In silico screening of protein-binding peptides with an application to developing peptide inhibitors against antibiotic resistance.PNAS nexus · 2024Article
- High-throughput discovery of inhibitory protein fragments with AlphaFold.bioRxiv : the preprint server for biology · 2024Article
- A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.Current medicinal chemistry · 2024Article
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- Prediction and Modeling of Protein-Protein Interactions Using "Spotted" Peptides with a Template-Based Approach.Biomolecules · 2022Article
- Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment.Journal of chemical information and modeling · 2022Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Improving Docking Power for Short Peptides Using Random Forest.Journal of chemical information and modeling · 2021Article
- Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm.BMC bioinformatics · 2021Article
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Authors and funding
2 authors.
Funding
Abstract
We present a nonredundant benchmark, coined PepPro, for testing peptide-protein docking algorithms. Currently, PepPro contains 89 nonredundant experimentally determined peptide-protein complex structures, with peptide sequence lengths ranging from 5 to 30 amino acids. The benchmark covers peptides with distinct secondary structures, including helix, partial helix, a mixture of helix and β-sheet, β-sheet formed through binding, β-sheet formed through self-folding, and coil. In addition, unbound proteins' structures are provided for 58 complexes and can be used for testing the ability of a docking algorithm handling the conformational changes of proteins during the binding process. PepPro should benefit the docking community for the development and improvement of peptide docking algorithms. The benchmark is available at http://zoulab.dalton.missouri.edu/PepPro_benchmark. © 2019 Wiley Periodicals, Inc.
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