ATPdock: a template-based method for ATP-specific protein-ligand docking.
Bioinformatics
; 38(2): 556-558, 2022 01 03.
Article
em En
| MEDLINE
| ID: mdl-34546290
ABSTRACT
MOTIVATION Accurately identifying protein-ATP binding poses is significantly valuable for both basic structure biology and drug discovery. Although many docking methods have been designed, most of them require a user-defined binding site and are difficult to achieve a high-quality protein-ATP docking result. It is critical to develop a protein-ATP-specific blind docking method without user-defined binding sites. RESULTS:
Here, we present ATPdock, a template-based method for docking ATP into protein. For each query protein, if no pocket site is given, ATPdock first identifies its most potential pocket using ATPbind, an ATP-binding site predictor; then, the template pocket, which is most similar to the given or identified pocket, is searched from the database of pocket-ligand structures using APoc, a pocket structural alignment tool; thirdly, the rough docking pose of ATP (rdATP) is generated using LS-align, a ligand structural alignment tool, to align the initial ATP pose to the template ligand corresponding to template pocket; finally, the Metropolis Monte Carlo simulation is used to fine-tune the rdATP under the guidance of AutoDock Vina energy function. Benchmark tests show that ATPdock significantly outperforms other state-of-the-art methods in docking accuracy. AVAILABILITY AND IMPLEMENTATION https//jun-csbio.github.io/atpdock/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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MEDLINE
Assunto principal:
Proteínas
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Trifosfato de Adenosina
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article