Dynamic Undocking: A Novel Method for Structure-Based Drug Discovery.
Methods Mol Biol
; 1824: 195-215, 2018.
Article
em En
| MEDLINE
| ID: mdl-30039408
ABSTRACT
Computer-aided methods have been broadly used in pharmaceutical research to identify potential ligands and design effective therapeutics. Most of the approaches rely on the binding affinity prediction and approximate thermodynamic properties of the system. Our alternative approach focuses on structural stability, provided by native protein-ligand interactions, in particular hydrogen bonds. Based on this idea, we designed new fast computational method, called dynamic undocking (DUck), that evaluates stability by calculating the work necessary to break the most important native contact in a ligand-receptor complex. This property is effective in distinguishing true ligands from decoys and is orthogonal to currently existing docking methods, thus making it exceptionally useful in virtual screening. Here, we present a protocol suitable for DUck's application in drug design strategy, as well as notes that will help to solve common problems addressed by users.
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Descoberta de Drogas
/
Simulação de Dinâmica Molecular
Tipo de estudo:
Guideline
Idioma:
En
Ano de publicação:
2018
Tipo de documento:
Article