Primary Citation PubMed: 9108479
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Assay strategies for the discovery and validation of therapeutics targeting Brugia pahangi Hsp90.
(2010) PLoS Negl Trop Dis 4
PubMed: 20559560 | PubMedCentral: PMC2886105 | DOI: 10.1371/journal.pntd.0000714
Points, mean; bars, s.d. ( D ) Overlay of GA-bound homology models (derived using Prime software of Schrodinger L.L.C, NY) of B. pahangi (orange, Accession number AJ005784) and C. elegans (green, Acce... sion number Z75530) and the X-ray crystal structure of human Hsp90α (blue, PDB ID: 1YET).
Publication Year: 2010
Development and validation of an improved algorithm for overlaying flexible molecules.
(2012) J Comput Aided Mol Des 26
PubMed: 22538643 | PubMedCentral: PMC3348445 | DOI: 10.1007/s10822-012-9573-y
14 True overlay of ten heat shock protein ligands, showing the poor volume overlap of three ligands (from PDB complexes 1byq, 1uy8, 1yet, coloured in magenta ) with the remainder (1yc1, 1yc4,... 2bsm, 2byi, 2bz5, 2cct, 2uwd, coloured in green ) Acetylcholinesterase This is the only protein on which we were entirely unsuccessful.
Heat shock protein 90 The 10 ligands in this set may be divided into two groups: (a) the closely similar pyrazole or isoxazole ligands of 1yc1, 1yc4, 2bsm, 2byi, 2bz5, 2cct, 2uwd together with the structurally unrelated ligand from 2bz5; and (b) two purine ligands (1byq and 1uy8) and the macrocyclic ligand from 1yet.
Table 1 Test sets Protein Number of complexes PDB codes Protein kinase 5 (PK5) 2 1v0o, 1v0p Fatty acid binding protein (FABP) 3 1tou, 1tow, 2hnx Neprilysin (NEP) 4 1dmt, 1r1h, 1r1j, 1y8j Dihydrofolate reductase (DHFR) 6 1drf, 1hfr, 1mvt, 1pd9, 1s3v, 2dhf Checkpoint kinase (Chk1) 16 1nvq, 1nvr, 1nvs, 1zlt, 1zys, 2br1, 2brb, 2brg, 2brh, 2brm, 2bro, 2c3l, 2cgu, 2cgw, 2cgx, 2hog Neuraminidase (NEU) 11 1a4g, 1a4q, 1b9s, 1b9t, 1b9v, 1inf, 1inv, 1ivb, 1nsc, 1nsd, 1vcj Carbonic anhydrase (CA) 13 1bn3, 1bn4, 1bnq, 1cim, 1eou, 1if7, 1oq5, 1xpz, 1zgf, 1zh9, 2eu3, 2hoc, 2nng Adenosine deaminase (ADA) 11 1krm, 1ndv, 1ndw, 1ndy, 1o5r, 1qxl, 1uml, 1v7a, 1v79, 1wxy, 2e1w Heat shock protein 90 (HSP) 10 1byq, 1uy8, 1yc1, 1yc4, 1yet, 2bsm, 2byi, 2bz5, 2cct, 2uwd Acetylcholinesterase (AChE) 11 1dx6, 1e66, 1eve, 1gpk, 1gpn, 1h23, 1w4l, 1zgb, 2ack, 2c5g, 2ckm Table 2 Test subsets Protein/subset Number of complexes PDB codes ADA/1 10 1ndv, 1ndw, 1ndy, 1o5r, 1qxl, 1uml, 1v7a, 1v79, 1wxy, 2e1w ADA/2 4 1o5r, 1qxl, 1uml, 1wxy ADA/3 4 1ndv, 1o5r, 1qxl, 1uml HSP/1 7 1yc1, 1yc4, 2bsm, 2byi, 2bz5, 2cct, 2uwd HSP/2 3 1byq, 1uy8, 2cct AChE/1 9 1dx6, 1e66, 1gpk, 1gpn, 1h23, 1w4l, 1zgb, 2ack, 2ckm AChE/2 4 1h23, 1w4l, 1zgb, 2ckm Ligand models were created with CORINA [ 38 ] with addition of required hydrogen atoms.
Publication Year: 2012
Chemo-informatic design of antibiotic geldenamycin analogs to target stress proteins HSP90 of pathogenic protozoan parasites.
(2013) Bioinformation 9
PubMed: 23750075 | PubMedCentral: PMC3669783 | DOI: 10.6026/97320630009329
The template (PDBID: 1YET) was selected.
As expected, HSP90 model structures were well superimposed onto each other and on the template (PDBID: 1YET) as well ( Figure 2 ).
Publication Year: 2013
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