Unknown

Dataset Information

0

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping.


ABSTRACT: BACKGROUND:Two recent technological advances dramatically reducing the rate of false-negatives in activity prediction by docking flexible 3D models of compounds include multi-conformational docking (mPockDock) and the docking of candidates to atomic property fields derived by co-crystallized ligands (mApfDock). RESULTS:The mApfDock and mPockDock provide the AUC of 90.4 and 83.8%, respectively. The mApfDock gave better performance when compounds required large induced-fit pocket changes unseen in crystallography, whereas the mPockDock is superior when the co-crystallized ligands do not represent sufficient chemical and binding location diversity. CONCLUSION:Both approaches proved to be efficient for scaffold hopping; they are complementary when the coverage of the co-crystallized complexes is poor but become convergent when the complexes are diverse enough.

SUBMITTER: Chen YC 

PROVIDER: S-EPMC4285145 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

altmetric image

Publications

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping.

Chen Yu-Chen YC   Totrov Max M   Abagyan Ruben R  

Future medicinal chemistry 20140101 16


<h4>Background</h4>Two recent technological advances dramatically reducing the rate of false-negatives in activity prediction by docking flexible 3D models of compounds include multi-conformational docking (mPockDock) and the docking of candidates to atomic property fields derived by co-crystallized ligands (mApfDock).<h4>Results</h4>The mApfDock and mPockDock provide the AUC of 90.4 and 83.8%, respectively. The mApfDock gave better performance when compounds required large induced-fit pocket ch  ...[more]

Similar Datasets

| S-EPMC4468813 | biostudies-literature
| S-EPMC2739202 | biostudies-literature
| S-EPMC5511031 | biostudies-literature
| S-EPMC6686534 | biostudies-other
| S-EPMC5963029 | biostudies-literature
| S-EPMC6096356 | biostudies-literature
| S-EPMC3328312 | biostudies-literature
| S-EPMC3125872 | biostudies-literature
| S-EPMC7404552 | biostudies-literature
| S-EPMC10708986 | biostudies-literature