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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

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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

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 str... cturally 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.

 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.

Publication Year: 2012

Variability in docking success rates due to dataset preparation.

(2012) J Comput Aided Mol Des 26

PubMed: 22566074 | PubMedCentral: PMC3397132 | DOI: 10.1007/s10822-012-9570-1

Table 2 Complexes requiring capping of chain termini or chain breaks Complexes requiring capping of chain termini  1GKC 1MEH 1Q41 1V48  1GM8 1 MMV 1R55 1V4S  1G... K 1 MZC 1R9O 1W1P  1HNN 1N1M 1S19 1W2G  1HP0 1N2J 1SJ0 1XM6  1HWI 1N2V 1SQN 1XOQ  1HWW 1N46 1T46 1XOZ  1IG3 1OF1 1T9B 1Y6B  1J3J 1OF6 1TT1 1YGC  1JD0 1OPK 1TZ8 1YQY  1JJE 1OQ5 1U1C 1YV3  1JLA 1OYT 1U4D 1YVF  1K3U 1P2Y 1UML 1YWR  1LPZ 1P62 1UNL 2BM2  1LRH 1PMN 1UOU 2BR1  1M2Z 1Q1G 1V0P 2BSM Complexes requiring capping of chain breaks  1GPK 1N46 1SJ0 1V48  1HP0 1NAV 1SQ5 1W2G  1HWI 1OF1 1SQN 1XM6  1J3J 1OF6 1T46 1XOQ  1JLA 1OYT 1T9B 1Y6B  1KE5 1P62 1U1C 1YV3  1L2S 1PMN 1U4D 1YWR  1MEH 1Q41 1UOU 1Z95  1MMV 1R9O 1V0P 2BR1 The ‘corrected’ ACS-Astex dataset After the session transpired at the ACS meeting, 3 structures from the ACS-Astex set (1GPK, 1HVY and 1S3V) were identified as containing an inverted stereocenter in the original dataset given to the participants compared to the original PDB structure.

Publication Year: 2012

Co-crystalization and in vitro biological characterization of 5-aryl-4-(5-substituted-2-4-dihydroxyphenyl)-1,2,3-thiadiazole Hsp90 inhibitors.

(2012) PLoS One 7

PubMed: 22984537 | PubMedCentral: PMC3439374 | DOI: 10.1371/journal.pone.0044642

For a variety of pyrazole and isoxazole inhibitors the conformation of the loop is either in an open (pdb 2BYI and 2BYH) or compact conformation (pdb 2CCU, 2VCJ, 2CCT, 2CCS, 2BSM and 2BT0).

Publication Year: 2012

High-Throughput parallel blind Virtual Screening using BINDSURF.

(2012) BMC Bioinformatics 13 Suppl 14

PubMed: 23095663 | PubMedCentral: PMC3504923 | DOI: 10.1186/1471-2105-13-S14-S13

a , we show how the strongest interaction spot (blue sphere) for chaperone Hsp90 (PDB: 2BSM ) coincides with crystal binding site.

Figure 3 Surface screening results for PDB: 2BSM .

Surface screening results for PDB: 2BSM .

Publication Year: 2012

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4477625

For the first case, four compounds were investigated starting from the structure of HSP90 in complex with one member of the series (VER49009; PDB ID: 2BSM, hence the usage of the ligand name BSM in th... s work) and editing the ligand substituents R1 and R2 accordingly.

Publication Year: 2015