17 0

Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites

Title
Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites
Author
하정미
Keywords
PROTEIN-LIGAND COMPLEXES; MOLECULAR DOCKING; DRUG DESIGN; HYDROPHOBIC ENCLOSURE; SCORING FUNCTIONS; FLEXIBLE DOCKING; PDBBIND DATABASE; METALLOPROTEINS; DISCOVERY; CHARGES
Issue Date
2009-10
Publisher
AMER CHEMICAL SOC
Citation
JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 49, No. 10, Page. 2382-2387
Abstract
Use of SiteMap for binding site classification and its connection to QM/MM (quantum mechanics/ molecular mechanics) docking performance were investigated.. Using the hydrophilic/hydrophobic character values along with balance between them which SiteMap calculates, we sorted 455 cocrystal complexes available from protein data bank into three groups and tested how Glide, a conventional docking program, and QPLD, a QM/MM docking program, perform on them. QPLD showed improvements on all three groups over Glide but with varying degrees. Analysis of the results was carried out, and establishment of correlations between the classification of binding sites and QM1MM docking performance was attempted. It was found that QM/ MM docking delivers the most improvements for primarily hydrophobic binding sites with substantial hydrophilic interactions. Based on our findings, we make suggestions for use of QM/MM docking and directions for further developments.
URI
https://pubs.acs.org/doi/abs/10.1021/ci900231phttp://repository.hanyang.ac.kr/handle/20.500.11754/104159
ISSN
1549-9596
DOI
10.1021/ci900231p
Appears in Collections:
COLLEGE OF PHARMACY[E](약학대학) > PHARMACY(약학과) > Articles
Files in This Item:
There are no files associated with this item.
Export
RIS (EndNote)
XLS (Excel)
XML


qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

BROWSE