Primary Citation PubMed: 10633045
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Training a scoring function for the alignment of small molecules.
(2010) J Chem Inf Model 50
PubMed: 20831240 | PubMedCentral: PMC2946173 | DOI: 10.1021/ci100227h
Out of the 57 ligands, only 4 do not have at least 2 out of these 3 features, and ligands 1DI8 , 1P5E , and 1WCC are among them.
( 31 ) If the six ligands 1DI8 , 1P5E , 1PKD , 1PXI , 1PXJ , and 1WCC were excluded, then our results would improve from 39.6% to 47.6% correct for the rigid-body alignments and from 22.4% to 26.6% correct for the flexible alignments.
Publication Year: 2010
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities.
(2011) Nucleic Acids Res 39
PubMed: 21051336 | PubMedCentral: PMC3013767 | DOI: 10.1093/nar/gkq878
Case study 1: identifying cyclin dependent kinases inhibitors As a test for the pharmacaphore searching routine we used the eight available structures of CDK complexes stored in the PDBbind database (... 27 ) with PDB codes 1AQ1, 1DI8, 1DM2, 1E1V, 1E1X, 1FVV, 1UNH and 2A4L.
Publication Year: 2011
A structure-guided approach for protein pocket modeling and affinity prediction.
(2013) J Comput Aided Mol Des 27
PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9
PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP,... 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.
Publication Year: 2013
PubMed ID is not available.
Published in 2015
PDB ID Resolution (Å) 1GZ8 1.30 1JVP 1.53 1H00 1.60 1OIT 1.60 1URW 1.60 1H01 1.79 1H08 1.80 1E1X 1.85 1H07 1.85 1H0V 1.90 1OIR 1.91 1E1V 1.95 1PXI 1.95 1JSV 1.96 1PXO 1.96 1AQ1 2.00 1GII 2.00 ... KE6 2.00 1KE7 2.00 1KE8 2.00 1KE9 2.00 1PYE 2.00 1R78 2.00 1CKP 2.05 1DM2 2.10 1H0W 2.10 1DI8 2.20 1FVT 2.20 1GIJ 2.20 1KE5 2.20 1W0X 2.20 1VYZ 2.21 1PXJ 2.30 1PXP 2.30 1OIQ 2.31 1V1K 2.31 1P2A 2.50 1PXL 2.50 1PXN 2.50 1PF8 2.51 1PXM 2.53 1G5S 2.61 1GIH 2.80 1PXK 2.80 The final score used to rank compounds was purposely designed to be the average score across these 44 structures of CDK2 so as to account for structural variability.
Publication Year: 2015
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