Validation of cycle conformation in small molecules

a 2022

Validation of cycle conformation in small molecules

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU a Radka SVOBODOVÁ

Základní údaje

Originální název

Validation of cycle conformation in small molecules

Autoři

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU a Radka SVOBODOVÁ

Vydání

XXI. Meeting of Biochemists and Molecular Biologists, 2022

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Přírodovědecká fakulta

Změněno: 1. 8. 2024 21:48, Mgr. Bc. Gabriela Bučeková

Anotace

V originále

The structural data of biomacromolecules are an essential input for various fields of science. The Protein Data Bank (PDB) contains more than 190,000 experimentally determined structures. The PDB database is one of the most widely used sources of three-dimensional structural data of macromolecules and small molecules - ligands. Although each molecular structure is validated before the deposition, some structures may contain minor or major errors. With the growth of the number of determined structures, it is necessary to pay more attention to data quality. A large number of biomacromolecule and ligand structure quality criteria are established. However, some of them are still not included in validation reports, such as validation of conformation of the cycle. Incorrect determination of the cycle conformation in the ligands may impact the geometric property of a macromolecule or molecular fragments in the surrounding area. We focused on the validation of basic cycles such as cyclopentane, cyclohexane and benzene. Firstly, we compare the experimentally determined conformation of the ligand from the PDB database with templates of ideal conformation of cycles. In the next step, we analysed the electron density coverage of each atom in the cycle. We analysed the occurrence of the untypical conformation of ligands. Subsequently, we examined the reasoning for selecting the energetically unfavoured conformations.

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

Citovat

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU a Radka SVOBODOVÁ. Validation of cycle conformation in small molecules. In XXI. Meeting of Biochemists and Molecular Biologists. 2022.

@proceedings{2421158,
   author = {Bučeková, Gabriela and Doshchenko, Viktoriia and Chareshneu, Aliaksei and Svobodová, Radka},
   booktitle = {XXI. Meeting of Biochemists and Molecular Biologists},
   language = {eng},
   title = {Validation of cycle conformation in small molecules},
   url = {https://setkani.sci.muni.cz/en},
   year = {2022}
}

TY  - CONF
ID  - 2421158
AU  - Bučeková, Gabriela - Doshchenko, Viktoriia - Chareshneu, Aliaksei - Svobodová, Radka
PY  - 2022
TI  - Validation of cycle conformation in small molecules
UR  - https://setkani.sci.muni.cz/en
N2  - The structural data of biomacromolecules are an essential input for various fields of science. The Protein Data Bank (PDB) contains more than 190,000 experimentally determined structures. The PDB database is one of the most widely used sources of three-dimensional structural data of macromolecules and small molecules - ligands. Although each molecular structure is validated before the deposition, some structures may contain minor or major errors. With the growth of the number of determined structures, it is necessary to pay more attention to data quality. A large number of biomacromolecule and ligand structure quality criteria are established. However, some of them are still not included in validation reports, such as validation of conformation of the cycle. Incorrect determination of the cycle conformation in the ligands may impact the geometric property of a macromolecule or molecular fragments in the surrounding area. We focused on the validation of basic cycles such as cyclopentane, cyclohexane and benzene. Firstly, we compare the experimentally determined conformation of the ligand from the PDB database with templates of ideal conformation of cycles. In the next step, we analysed the electron density coverage of each atom in the cycle. We analysed the occurrence of the untypical conformation of ligands. Subsequently, we examined the reasoning for selecting the energetically unfavoured conformations.
ER  -

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU a Radka SVOBODOVÁ. Validation of cycle conformation in small molecules. In \textit{XXI. Meeting of Biochemists and Molecular Biologists}. 2022.

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