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20231222212604.0 |
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231222s2003 xx ||||| 00| ||eng c |
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|a pubmed24n0423.xml
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|a (DE-627)NLM126777322
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|a (NLM)12925999
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|a DE-627
|b ger
|c DE-627
|e rakwb
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| 041 |
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|a eng
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| 100 |
1 |
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|a Wu, Guosheng
|e verfasserin
|4 aut
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| 245 |
1 |
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|a Detailed analysis of grid-based molecular docking
|b A case study of CDOCKER-A CHARMm-based MD docking algorithm
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| 264 |
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|c 2003
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|a Text
|b txt
|2 rdacontent
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|a ohne Hilfsmittel zu benutzen
|b n
|2 rdamedia
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|a Band
|b nc
|2 rdacarrier
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| 500 |
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|a Date Completed 24.02.2004
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|a Date Revised 31.03.2022
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|a published: Print
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|a Citation Status MEDLINE
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|a Copyright 2003 Wiley Periodicals, Inc.
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|a The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures
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| 650 |
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|a Journal Article
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| 650 |
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|a Research Support, Non-U.S. Gov't
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| 650 |
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|a Research Support, U.S. Gov't, P.H.S.
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| 650 |
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7 |
|a Ligands
|2 NLM
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| 650 |
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|a Proteins
|2 NLM
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| 700 |
1 |
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|a Robertson, Daniel H
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Brooks, Charles L
|c 3rd
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Vieth, Michal
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 24(2003), 13 vom: 25. Okt., Seite 1549-62
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:24
|g year:2003
|g number:13
|g day:25
|g month:10
|g pages:1549-62
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|a GBV_USEFLAG_A
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| 912 |
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|a SYSFLAG_A
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| 912 |
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|a GBV_NLM
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| 912 |
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|a GBV_ILN_350
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| 951 |
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|a AR
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| 952 |
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|d 24
|j 2003
|e 13
|b 25
|c 10
|h 1549-62
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