Exploring cooperative molecular contacts using a PostgreSQL database system.
Mol Inform
; 42(5): e2200235, 2023 05.
Article
em En
| MEDLINE
| ID: mdl-36653303
ABSTRACT
Cooperative molecular contacts play an important role in protein structure and ligand binding. Here, we constructed a PostgreSQL database that stores structural information in the form of atomic environments and allows flexible mining of molecular contacts. Taking the Ser-His-Asp/Glu catalytic triad as a first test case, we demonstrate that the presence of a carboxylate oxygen atom in the vicinity of a His is associated with shorter Ser-OH..N-His bond in the PDB30 subset. We prospectively mine catalytic triads in unannotated proteins, suggesting catalytic functions for unannotated proteins. As a second test case, we demonstrate that this database system can include ligand atoms, represented by Sybyl atom types, by evaluating the proportion of counter-ions for ligand carboxylate oxygens.
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MEDLINE
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Proteínas
Idioma:
En
Ano de publicação:
2023
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Article