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231223s2005 xx ||||| 00| ||eng c |
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|a DE-627
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|a eng
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| 100 |
1 |
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|a Bindewald, Eckart
|e verfasserin
|4 aut
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| 245 |
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|a A scoring function for docking ligands to low-resolution protein structures
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|c 2005
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| 336 |
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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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| 338 |
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|a Band
|b nc
|2 rdacarrier
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| 500 |
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|a Date Completed 31.03.2005
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|a Date Revised 21.11.2008
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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 Copyright 2005 Wiley Periodicals, Inc.
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|a We present a docking method that uses a scoring function for protein-ligand docking that is designed to maximize the docking success rate for low-resolution protein structures. We find that the resulting scoring function parameters are very different depending on whether they were optimized for high- or low-resolution protein structures. We show that this docking method can be successfully applied to predict the ligand-binding site of low-resolution structures. For a set of 25 protein-ligand complexes, in 76% of the cases, more than 50% of ligand-contacting residues are correctly predicted (using receptor crystal structures where the binding site is unspecified). Using decoys of the receptor structures having a 4 A RMSD from the native structure, for the same set of complexes, in 72% of the cases, we obtain at least one correctly predicted ligand-contacting residue. Furthermore, using an 81-protein-ligand set described by Jain, in 76 (93.8%) cases, the algorithm correctly predicts more than 50% of the ligand-contacting residues when native protein structures are used. Using 3 A RMSD from native decoys, in all but two cases (97.5%), the algorithm predicts at least one ligand-binding residue correctly. Finally, compared to the previously published Dolores method, for 298 protein-ligand pairs, the number of cases in which at least half of the specific contacts are correctly predicted is more than four times greater
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| 650 |
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|a Journal Article
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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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| 700 |
1 |
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|a Skolnick, Jeffrey
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 26(2005), 4 vom: 01. März, Seite 374-83
|w (DE-627)NLM098138448
|x 0192-8651
|7 nnns
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| 773 |
1 |
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|g volume:26
|g year:2005
|g number:4
|g day:01
|g month:03
|g pages:374-83
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| 952 |
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|d 26
|j 2005
|e 4
|b 01
|c 03
|h 374-83
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