ArticleCurrent medicinal chemistry2024
A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.
Article in Current medicinal chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed, 16 citations in OpenAlex.
- Structure-based identification, phosphorylation, cyclization and engineering of a self-binding peptide carboxy-terminal to EGFR kinase domain by integrating dynamics simulation, energetics calculation and fluorescence analysis.European biophysics journal : EBJ · 2026Article
- Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay.European biophysics journal : EBJ · 2025Article
- Computational Methods and Artificial Intelligence in the Discovery and Development of Therapeutic Peptides and Beyond.Current medicinal chemistry · 2024Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPeptides play crucial roles in diverse cellular functions and participate in many biological processes by interacting with a variety of proteins, which have also been exploited as a promising class of therapeutic agents to target druggable proteins over the past decades. Understanding the intrinsic association between the structure and affinity of protein-peptide interactions (PpIs) should be considerably valuable for the computational peptidology area, such as guiding protein-peptide docking calculations, developing protein-peptide affinity scoring functions, and designing peptide ligands for specific protein receptors.
objectiveWe attempted to create a data source for relating PpI structure to affinity.
methodsBy exhaustively surveying the whole protein data bank (PDB) database as well as the ontologically enriched literature information, we manually curated a structure- based data set of protein-peptide affinities, PpI[S/A]
resultsThe collected structures were resolved at a high-resolution level with either Xray crystallography or solution NMR, while the deposited affinities were characterized by dissociation constant, i.e. K
conclusionThe PpI[S/A]
Indexed as
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Registered trials
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