Chapter title |
Dynamic Undocking: A Novel Method for Structure-Based Drug Discovery
|
---|---|
Chapter number | 11 |
Book title |
Rational Drug Design
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-8630-9_11 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8629-3, 978-1-4939-8630-9
|
Authors |
Maciej Majewski, Sergio Ruiz-Carmona, Xavier Barril, Majewski, Maciej, Ruiz-Carmona, Sergio, Barril, Xavier |
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. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 18 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 5 | 28% |
Researcher | 4 | 22% |
Student > Doctoral Student | 2 | 11% |
Professor | 2 | 11% |
Student > Master | 2 | 11% |
Other | 2 | 11% |
Unknown | 1 | 6% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 7 | 39% |
Chemistry | 4 | 22% |
Pharmacology, Toxicology and Pharmaceutical Science | 2 | 11% |
Agricultural and Biological Sciences | 1 | 6% |
Unspecified | 1 | 6% |
Other | 2 | 11% |
Unknown | 1 | 6% |