Workshop: Software tools for structural bioinformatics
Radka Svobodová from the Structural Bioinformatics group organized a workshop, Software Tools for Structural Bioinformatics, on 12-14 February.
A preprint about the validation of ring conformation was published
Protein structures are highly valuable for research. A key point for their applicability is their quality. An important facet of structure quality is the validation of ligands. Validation of ring conformation has yet to be comprehensively performed despite rings strongly influencing the formation of the ligand’s scaffold and shape. Therefore, the most stable conformations occur frequently in nature and should be found in Protein Data Bank (PDB) structures.
Our colleagues Gabriela, Viktoriia, Aliaksei, Jana, Michal, Tomáš, Vladimír, and Radka examined which conformations of rings occur in PDB structures. The analysis focused on conformations of all cyclopentane, cyclohexane, and benzene rings. They found that most rings (98.32 %) have energetically favourable conformations. The existence of most of the energetically unfavourable ring conformations (1.68 %) is not supported by experimental data.
The preprint of the article Rare ring conformations in PDB: Facts or wishful thinking? is available in bioRχiv.
