AHoJ-DB: A PDB-wide Assignment of apo & holo Relationships Based on Individual Protein-Ligand Interactions

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F24%3A00585153" target="_blank" >RIV/61388963:_____/24:00585153 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11320/24:10487125 RIV/00216208:11310/24:10487125

Result on the web

<a href="https://doi.org/10.1016/j.jmb.2024.168545" target="_blank" >https://doi.org/10.1016/j.jmb.2024.168545</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jmb.2024.168545" target="_blank" >10.1016/j.jmb.2024.168545</a>

Result language

angličtina

Original language name

AHoJ-DB: A PDB-wide Assignment of apo & holo Relationships Based on Individual Protein-Ligand Interactions

Original language description

A single protein structure is rarely sufficient to capture the conformational variability of a protein. Both bound and unbound (holo and apo) forms of a protein are essential for understanding its geometry and making meaningful comparisons. Nevertheless, docking or drug design studies often still consider only single protein structures in their holo form, which are for the most part rigid. With the recent explosion in the field of structural biology, large, curated datasets are urgently needed. Here, we use a previously developed application (AHoJ) to perform a comprehensive search for apo-holo pairs for 468,293 biologically relevant protein-ligand interactions across 27,983 proteins. In each search, the binding pocket is captured and mapped across existing structures within the same UniProt, and the mapped pockets are annotated as apo or holo, based on the presence or absence of ligands. We assemble the results into a database, AHoJ-DB (www.apoholo.cz/db), that captures the variability of proteins with identical sequences, thereby exposing the agents responsible for the observed differences in geometry. We report several metrics for each annotated pocket, and we also include binding pockets that form at the interface of multiple chains. Analysis of the database shows that about 24% of the binding sites occur at the interface of two or more chains and that less than 50% of the total binding sites processed have an apo form in the PDB. These results can be used to train and evaluate predictors, discover potentially druggable proteins, and reveal protein- and ligand-specific relationships that were previously obscured by intermittent or partial data. Availability: www.apoholo.cz/db.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2024

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Molecular Biology

ISSN

0022-2836

e-ISSN

1089-8638

Volume of the periodical

436

Issue of the periodical within the volume

17

Country of publishing house

NL - THE KINGDOM OF THE NETHERLANDS

Number of pages

9

Pages from-to

168545

UT code for WoS article

001331535400001

EID of the result in the Scopus database

2-s2.0-85188992065