1xep

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[[Image:1xep.gif|left|200px]]
[[Image:1xep.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1xep |SIZE=350|CAPTION= <scene name='initialview01'>1xep</scene>, resolution 1.55&Aring;
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The line below this paragraph, containing "STRUCTURE_1xep", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span>
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or leave the SCENE parameter empty for the default display.
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|GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
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-->
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|DOMAIN=
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{{STRUCTURE_1xep| PDB=1xep | SCENE= }}
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|RELATEDENTRY=[[1lgu|1LGU]], [[1li2|1LI2]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xep OCA], [http://www.ebi.ac.uk/pdbsum/1xep PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xep RCSB]</span>
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}}
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'''Catechol in complex with T4 lysozyme L99A/M102Q'''
'''Catechol in complex with T4 lysozyme L99A/M102Q'''
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[[Category: Graves, A P.]]
[[Category: Graves, A P.]]
[[Category: Shoichet, B K.]]
[[Category: Shoichet, B K.]]
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[[Category: bacteriolytic enzyme]]
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[[Category: Bacteriolytic enzyme]]
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[[Category: glycosidase]]
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[[Category: Glycosidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:55:55 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:48:36 2008''
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Revision as of 11:55, 3 May 2008

Template:STRUCTURE 1xep

Catechol in complex with T4 lysozyme L99A/M102Q


Overview

Molecular docking is widely used to predict novel lead compounds for drug discovery. Success depends on the quality of the docking scoring function, among other factors. An imperfect scoring function can mislead by predicting incorrect ligand geometries or by selecting nonbinding molecules over true ligands. These false-positive hits may be considered "decoys". Although these decoys are frustrating, they potentially provide important tests for a docking algorithm; the more subtle the decoy, the more rigorous the test. Indeed, decoy databases have been used to improve protein structure prediction algorithms and protein-protein docking algorithms. Here, we describe 20 geometric decoys in five enzymes and 166 "hit list" decoys-i.e., molecules predicted to bind by our docking program that were tested and found not to do so-for beta-lactamase and two cavity sites in lysozyme. Especially in the cavity sites, which are very simple, these decoys highlight particular weaknesses in our scoring function. We also consider the performance of five other widely used docking scoring functions against our geometric and hit list decoys. Intriguingly, whereas many of these other scoring functions performed better on the geometric decoys, they typically performed worse on the hit list decoys, often highly ranking molecules that seemed to poorly complement the model sites. Several of these "hits"from the other scoring functions were tested experimentally and found, in fact, to be decoys. Collectively, these decoys provide a tool for the development and improvement of molecular docking scoring functions. Such improvements may, in turn, be rapidly tested experimentally against these and related experimental systems, which are well-behaved in assays and for structure determination.

About this Structure

1XEP is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.

Reference

Decoys for docking., Graves AP, Brenk R, Shoichet BK, J Med Chem. 2005 Jun 2;48(11):3714-28. PMID:15916423 Page seeded by OCA on Sat May 3 14:55:55 2008

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