Abstract
We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein-ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu).
| Original language | American English |
|---|---|
| Pages (from-to) | 295-301 |
| Number of pages | 7 |
| Journal | Protein Science |
| Volume | 25 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 1 2016 |
| Externally published | Yes |
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
Keywords
- computational docking
- computer-aided drug design
- covalent inhibitors
- ligand-protein interactions
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