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PEPCONF, a diverse data set of peptide conformational energies.

ABSTRACT: 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-?PBE-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.

SUBMITTER: Prasad VK

PROVIDER: S-EPMC6343515 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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PEPCONF, a diverse data set of peptide conformational energies.

Prasad Viki Kumar VK Otero-de-la-Roza Alberto A Otero-de-la-Roza Alberto A DiLabio Gino A GA

Scientific data 20190122

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 ...[more]

PMID: 30667382

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Project description:We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient (RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy.

Dataset Information

PEPCONF, a diverse data set of peptide conformational energies.

Publications

PEPCONF, a diverse data set of peptide conformational energies.

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