Validation of cycle conformation in Protein Data Bank
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| Year of publication | 2020 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | Biomacromolecular structural data are key results of modern life scienc-es. Most structures of biomacromolecules and their ligands are accessible via the Protein Data Bank (PDB) database. However, some structures were found to contain serious errors. This discovery showed the importance of validation of biomacromolecular complexes. First validation approaches focused on geometric properties of standard biomacromolecular residues (i.e., amino acids, nucleotides). This validation approach was later extended to validate ligands. A step forward in validation was the release of PDB validation reports for almost every structure. A still uncovered topic in this field is a validation of cycle conformation. In our work, we focus on this topic, specifically: We went through all samples of basic cycles (i.e., cyclopentane, cyclohexane, benzen), occurring in Protein Data Bank and performed an analysis of their conformations. We found many occurences of energetically unfavoured conformations. For them, we analysed in detail the experimental data (i.e., electron densities) and examined if the conformation has a biological reasoning. |
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