Name
Title | ||
|---|---|---|
Docking and scoring with ICM: the benchmarking results and strategies for improvement. |
Abstract | ||
|---|---|---|
Flexible docking and scoring using the internal coordinate mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The ICM virtual ligand screening was tested against the 40 DUD target benchmarks and 11-target WOMBAT sets. The self-docking accuracy was evaluated for the top 1 and top 3 scoring poses at each ligand binding site with near native conformations below 2 Å RMSD found in 91 and 95% of the predictions, respectively. The virtual ligand screening using single rigid pocket conformations provided the median area under the ROC curves equal to 69.4 with 22.0% true positives recovered at 2% false positive rate. Significant improvements up to ROC AUC = 82.2 and ROC((2%)) = 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1007/s10822-012-9547-0 | Journal of computer-aided molecular design |
Keywords | Field | DocType |
Docking,Scoring,Virtual ligand screening,Structure-based drug design,ICM,Internal coordinate mechanics | False positive rate,Receiver operating characteristic,Docking (dog),Ligand (biochemistry),Chemistry,Bioinformatics,Virtual screening,True positive rate,Benchmarking | Journal |
Volume | Issue | ISSN |
26 | 6 | 1573-4951 |
Citations | PageRank | References |
24 | 0.96 | 17 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Marco A C Neves | 1 | 32 | 2.23 |
| Maxim Totrov | 2 | 269 | 31.59 |
| Ruben Abagyan | 3 | 430 | 55.44 |