5ozu: Difference between revisions
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==Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 41== | ==Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 41== | ||
<StructureSection load='5ozu' size='340' side='right' caption='[[5ozu]], [[Resolution|resolution]] 1.12Å' scene=''> | <StructureSection load='5ozu' size='340' side='right'caption='[[5ozu]], [[Resolution|resolution]] 1.12Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ozu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OZU OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[5ozu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OZU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OZU FirstGlance]. <br> | ||
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr> | </td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ozu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ozu OCA], [http://pdbe.org/5ozu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ozu RCSB], [http://www.ebi.ac.uk/pdbsum/5ozu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ozu ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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[[Category: Cryphonectria parasitica]] | [[Category: Cryphonectria parasitica]] | ||
[[Category: Endothiapepsin]] | [[Category: Endothiapepsin]] | ||
[[Category: Large Structures]] | |||
[[Category: Heine, A]] | [[Category: Heine, A]] | ||
[[Category: Klebe, G]] | [[Category: Klebe, G]] | ||
Revision as of 10:35, 2 September 2020
Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 41Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 41
Structural highlights
Publication Abstract from PubMedToday the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that approximately 25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods. High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.,Schiebel J, Krimmer SG, Rower K, Knorlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glockner S, Weiss MS, Mueller U, Klebe G, Heine A Structure. 2016 Aug 2;24(8):1398-409. doi: 10.1016/j.str.2016.06.010. Epub 2016, Jul 21. PMID:27452405[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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