2f1b: Difference between revisions

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==Overview==

Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is, a promising target for drug development in anti-tumor therapies. Using, X-ray crystallography, we have determined the structure of Drosophila, melanogaster GMII (dGMII) complexed with three different inhibitors, exhibiting IC50's ranging from 80 to 1000 microM. These structures, along, with those of seven other available dGMII/inhibitor complexes, were then, used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small, inhibitors could be accurately docked by most of the software, while, docking of larger compounds (i.e., those with extended aromatic cycles or, long aliphatic chains) was more problematic. Overall, Glide provided the, best docking results, with the most accurately predicted binding around, the active site zinc atom. Further evaluation of Glide's performance, revealed its ability to extract active compounds from a benchmark library, of decoys.

Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.

==About this Structure==

Line 14:

[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]

[[Category: Single protein]]

[[Category: Kuntz, D.A.]]

[[Category: Kuntz, D A.]]

[[Category: Rose, D.R.]]

[[Category: Rose, D R.]]

[[Category: GB3]]

[[Category: MPD]]

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[[Category: glycosyl hydrolase family 38]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:16:43 2008''

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@@ Line 4: / Line 4: @@
 ==Overview==
-Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is, a promising target for drug development in anti-tumor therapies. Using, X-ray crystallography, we have determined the structure of Drosophila, melanogaster GMII (dGMII) complexed with three different inhibitors, exhibiting IC50's ranging from 80 to 1000 microM. These structures, along, with those of seven other available dGMII/inhibitor complexes, were then, used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small, inhibitors could be accurately docked by most of the software, while, docking of larger compounds (i.e., those with extended aromatic cycles or, long aliphatic chains) was more problematic. Overall, Glide provided the, best docking results, with the most accurately predicted binding around, the active site zinc atom. Further evaluation of Glide's performance, revealed its ability to extract active compounds from a benchmark library, of decoys.
+Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.
 ==About this Structure==
@@ Line 14: / Line 14: @@
 [[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
 [[Category: Single protein]]
-[[Category: Kuntz, D.A.]]
+[[Category: Kuntz, D A.]]
-[[Category: Rose, D.R.]]
+[[Category: Rose, D R.]]
 [[Category: GB3]]
 [[Category: MPD]]
@@ Line 22: / Line 22: @@
 [[Category: glycosyl hydrolase family 38]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:40:34 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:16:43 2008''