Validation of cycle conformation in Protein Data Bank

BUČEKOVÁ, Gabriela, Michal PAJTINKA a Radka SVOBODOVÁ. Validation of cycle conformation in Protein Data Bank. In ELIXIR CZ Annual Conference 2020. 2020.

Základní údaje

• Originální název: Validation of cycle conformation in Protein Data Bank
• Autoři: BUČEKOVÁ, Gabriela, Michal PAJTINKA a Radka SVOBODOVÁ.
• Vydání: ELIXIR CZ Annual Conference 2020, 2020.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Konferenční abstrakt
• Obor: 10608 Biochemistry and molecular biology
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Organizační jednotka: Přírodovědecká fakulta

Anotace

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.

Návaznosti

• LM2018131, projekt VaV: Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data