原创力文档Can We Trust king Results Evaluation of Seven Commonly Used Programs on PDBbind Database英文文献.pdfVIP
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Review
Can We Trust Docking Results? Evaluation of Seven
Commonly Used Programs on PDBbind Database
DARIUSZ PLEWCZYNSKI,1* ´ 1,2* RAFAŁ AUGUSTYNIAK,1,2 KRZYSZTOF GINALSKI1
MICHAŁ ŁAZNIEWSKI,
1Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw,
Pawinskiego 5a Street, 02-106 Warsaw, Poland
2Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw,
Banacha 1 Street, 02-097 Warsaw, Poland
Received 13 May 2010; Revised 30 June 2010; Accepted 1 July 2010
DOI 10.1002/jcc.21643
Published online in Wiley Online Library ().
Abstract: Docking is one of the most commonly used techniques in drug design. It is used for both identifying
correct poses of a ligand in the binding site of a protein as well as for the estimation of the strength of protein–
ligand interaction. Because millions of compounds must be screened, before a suitable target for biological testing
can be identified, all calculations should be done in a reasonable time frame. Thus, all programs currently in use
exploit empirically based algorithms, avoiding systematic search of the conformational space. Similarly, the scoring
is done using simple equations, which makes it possible to speed up the entire process. Therefore, docking results
hav
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