Journal of Computer-Aided Molecular Design· 2012Q2
Variability in docking success rates due to dataset preparation
- 472citations
- Q2SCImago
- 2012year
Short summary
A 0.5 kcal/mol error in dataset preparation can cause over 20% fluctuations in molecular docking success rates, with missing bound waters identified as a key cause of docking failures.
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Key points
- A 0.5 kcal/mol dataset preparation error caused >20% fluctuations in docking success rates.
- MOE software with GBVI/WSA dG scoring achieved top-scoring poses within 2 Å of X-ray structures for 80% of Astex targets.
- 91% of targets had a pose within 2 Å in the top 30 poses.
- Docking failures were largely attributed to the absence of bound waters in the source dataset.
AI-generated from the title and abstract; the full text is not read.
Abstract
The results of cognate docking with the prepared Astex dataset provided by the organizers of the "Docking and Scoring: A Review of Docking Programs" session at the 241st ACS national meeting are presented. The MOE software with the newly developed GBVI/WSA dG scoring function is used throughout the study. For 80 % of the Astex targets, the MOE docker produces a top-scoring pose within 2 Å of the X-ray structure. For 91 % of the targets a pose within 2 Å of the X-ray structure is produced in the top 30 poses. Docking failures, defined as cases where the top scoring pose is greater than 2 Å from the experimental structure, are shown to be largely due to the absence of bound waters in the source dataset, highlighting the need to include these and other crucial information in future standardized sets. Docking success is shown to depend heavily on data preparation. A "dataset preparation" error of 0.5 kcal/mol is shown to cause fluctuations of over 20 % in docking success rates.
The authors' abstract, as published at the source. Journal of Computer-Aided Molecular Design, 2012 · DOI ↗
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RadiationPhysics and Astronomy