Ramachandran plots from the PeptideCs dataset

Description

Left panel shows energies of dipeptide with respect to main chain dihedral angles of first or second residue (option "Dihedrals") in 20° by 20° bins. The white dot shows the position of the structure with lowest energy (i.e. global minimum if "all" structures are selected). The white circle shows the currently selected bin.

Middle panel shows 3D model of the lowest structure in the bin, selected by hovering mouse (to avoid changing structure press and hold left mouse button while in the panel area) over the left panel (shown by white circle), its main chain dihedral angles, and the corresponging XYZ coordinates with the structure ID in the PeptideCs dataset.

Right panel shows the energy distribution of all structures within the 20° by 20° bin selected by mouse from the left panel. If "all" structures option is chosen, energies of constrained and optimized structures are distinguished by color. All structures higher than 99 kcal mol-1 are included in the 99 kcal mol-1 bin.

Residue 1:
Residue 2:
Dihedrals:
Displayed energies:
Structures to include:
Water solvation model:
3D Structure

Options

Residue 1, Residue 2:

The amino acid residues defining the dipeptide. "H" denotes the protonated histidine form, whereas "Hδ" and "Hɛ" are the two neutral forms with protonated "Nδ" and "Nɛ", respectively.

Dihedrals:

Energy surface of which amino acid residue (first or second, from N-terminus) is depicted.

Structures to include:

If "only constrained" option is chosen, the energy surface constructed of constrained structures only is depicted. "All" means that showed energy surface is constructed from all structures, including minimized.

Water solvation model:

Whether energy surface constructed from the energies calculated using either COSMO or COSMO-RS solvation model should be shown.

Displayed energies:

If "lowest" is chosen, the energy surface is constructed using the lowest energy in each 20° by 20° bin. "1st percentile" means the 1st percentile of the energies of each 20° by 20° bin is used for the energy surface construction.

Citation

Kalvoda T.; Culka, M.; Rulíšek, L.; Andris, E. Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method, J. Phys. Chem. B 2022 doi:10.1021/acs.jpcb.2c02861.

Underlying dataset is available at http://doi.org/10.25452/figshare.plus.19607172