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231223s2008 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.20917
|2 doi
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|a pubmed25n0593.xml
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|a (DE-627)NLM177795042
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|a (NLM)18293308
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|a DE-627
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|e rakwb
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| 041 |
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|a eng
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| 100 |
1 |
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|a Brylinski, Michal
|e verfasserin
|4 aut
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| 245 |
1 |
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|a Q-Dock
|b Low-resolution flexible ligand docking with pocket-specific threading restraints
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| 264 |
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|c 2008
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
|b cr
|2 rdacarrier
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| 500 |
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|a Date Completed 07.08.2008
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|a Date Revised 20.10.2021
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|a published: Print
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|a Citation Status MEDLINE
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| 520 |
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|a (c) 2008 Wiley Periodicals, Inc. J Comput Chem, 2008.
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|a The rapidly growing number of theoretically predicted protein structures requires robust methods that can utilize low-quality receptor structures as targets for ligand docking. Typically, docking accuracy falls off dramatically when apo or modeled receptors are used in docking experiments. Low-resolution ligand docking techniques have been developed to deal with structural inaccuracies in predicted receptor models. In this spirit, we describe the development and optimization of a knowledge-based potential implemented in Q-Dock, a low-resolution flexible ligand docking approach. Self-docking experiments using crystal structures reveals satisfactory accuracy, comparable with all-atom docking. All-atom models reconstructed from Q-Dock's low-resolution models can be further refined by even a simple all-atom energy minimization. In decoy-docking against distorted receptor models with a root-mean-square deviation, RMSD, from native of approximately 3 A, Q-Dock recovers on average 15-20% more specific contacts and 25-35% more binding residues than all-atom methods. To further improve docking accuracy against low-quality protein models, we propose a pocket-specific protein-ligand interaction potential derived from weakly homologous threading holo-templates. The success rate of Q-Dock employing a pocket-specific potential is 6.3 times higher than that previously reported for the Dolores method, another low-resolution docking approach
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| 650 |
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|a Journal Article
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| 650 |
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|a Research Support, N.I.H., Extramural
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| 650 |
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|a Ligands
|2 NLM
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| 650 |
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|a Proteins
|2 NLM
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| 650 |
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|a Receptors, Cell Surface
|2 NLM
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| 700 |
1 |
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|a Skolnick, Jeffrey
|e verfasserin
|4 aut
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| 773 |
0 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 29(2008), 10 vom: 30. Juli, Seite 1574-88
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:29
|g year:2008
|g number:10
|g day:30
|g month:07
|g pages:1574-88
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.20917
|3 Volltext
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