An important part of protein structures is their ligands. The conformation of rings in ligands is crucial for the ligands’ scaffold and shape and, therefore, for interactions with their surroundings and the subsequent biological function.
To address this, the Structural Bioinformatics research group developed a workflow to detect conformations of cyclohexane, cyclopentane, and benzene rings. The workflow can process rings originating from ligands, which are parts of experimental protein structures deposited in the Protein Data Bank and determined by X-ray crystallography. This fully automatic workflow utilises the Hill-Reilly approach to calculate puckering angles that quantitatively describe ring conformation. The reproducibility of the workflow is guaranteed by storing datasets within Onedata, which enables automatic dataset retrieval and the workflow execution.
The article titled Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach was recently published in the Journal of Cheminformatics.
Atomic Charge Calculator III, tool for calculation of partial atomic charges for various molecular systems, including small organic molecules and proteins, was published in the journal Nucleic Acids Research.
Our colleague Adrián Rošinec recently attended the conference CS3 2026 - Cloud Storage Synchronization and Sharing with a presentation about the Distributed data sharing infrastructure for scientific institute based on Onedata.
