Abstract：
:Virtual screening of small molecules against a protein target often identifies the correct pose, but the ranking in terms of binding energy remains a difficult problem, resulting in unacceptable numbers of false positives and negatives. To investigate this problem, the performance of three docking programs, FRED, QXP/FLO, and GLIDE, along with their five different scoring functions, was evaluated with the engineered cavity in cytochrome c peroxidase (CCP). This small cavity is negatively charged and completely buried from solvent. A test set of 60 molecules, experimentally identified as 43 "binders" and 17 "non-binders", were tested with the CCP binding site. The docking methods' performance is quantified by the ROC curve and their reproduction of crystal poses. The effects from generation of different ligand tautomers and inclusion of water molecule in the cavity are also discussed.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Deng W,Verlinde CLdoi
10.1021/ci800154wsubject
Has Abstractpub_date
2008-10-01 00:00:00pages
2010-20issue
10eissn
1549-9596issn
1549-960Xjournal_volume
48pub_type
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