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PEPCONF, a diverse data set of peptide conformational energies.

Viki Kumar PrasadAlberto Otero-de-la-RozaGino A DiLabio
Published in: Scientific data (2019)
We present an extensive and diverse database of peptide conformational energies. Our database contains five different classes of model geometries: dipeptides, tripeptides, and disulfide-bridged, bioactive, and cyclic peptides. In total, the database consists of 3775 conformational energy data points and 4530 conformer geometries. All the reference energies have been calculated at the LC-ωPBE-XDM/aug-cc-pVTZ level of theory, which is shown to yield conformational energies with an accuracy in the order of tenths of a kcal/mol when compared to complete-basis-set coupled-cluster reference data. The peptide conformational data set (PEPCONF) is presented as a high-quality reference set for the development and benchmarking of molecular-mechanics and semi-empirical electronic structure methods, which are the most commonly used techniques in the modeling of medium to large proteins.
Keyphrases
  • molecular dynamics
  • single molecule
  • molecular dynamics simulations
  • density functional theory
  • electronic health record
  • big data
  • machine learning
  • mass spectrometry
  • data analysis
  • liquid chromatography