Primary Citation PubMed: 11604388
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Toward the estimation of the absolute quality of individual protein structure models.
(2011) Bioinformatics 27
PubMed: 21134891 | PubMedCentral: PMC3031035 | DOI: 10.1093/bioinformatics/btq662
Three protein structures have in the meantime been superseded by newer entries in the PDB: 1un7 has been replaced by 2vhl, 1nrh by 1u8x and 1jsv by 2afb.
Publication Year: 2011
Hydrogen bonding penalty upon ligand binding.
(2011) PLoS One 6
PubMed: 21698148 | PubMedCentral: PMC3117785 | DOI: 10.1371/journal.pone.0019923
It has also been observed that larger HBPs appear in some X-ray structures, e.g., the structures of PDB code 3KVX and 1JSV, and the large values actually originate from poor fitting of small molecules... to the density, a common problem in crystallography  which can be manifested by clash of atoms.
ReFlexIn: a flexible receptor protein-ligand docking scheme evaluated on HIV-1 protease.
(2012) PLoS One 7
PubMed: 23110159 | PubMedCentral: PMC3480487 | DOI: 10.1371/journal.pone.0048008
The last three non-binders correspond to ligands that bind to protein kinases (ligands from pdb ID's 1FMO, 1FVV, and 1JSV).
Publication Year: 2012
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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