Primary Citation PubMed: 7844831
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AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
(2008) BMC Bioinformatics 9
PubMed: 18925937 | PubMedCentral: PMC2588602 | DOI: 10.1186/1471-2105-9-438
Some of the active compounds were taken from the PDB protein-ligand structures: 2 for ER (1err, 3ert; resolution 2.60 Å, 1.90 Å, respectively) and 10 for NA (1inf, 1inv, 1ivb, 1vcj, 1b... s, 1b9t, 1b9v, 1a4g, 1f8b, 2qwk; resolution 2.35–2.50 Å).
Publication Year: 2008
Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
(2009) BMC Bioinformatics 10
PubMed: 19671127 | PubMedCentral: PMC2739202 | DOI: 10.1186/1471-2105-10-245
Concerning NA, the query ligand was extracted from structure 1INV .
This is particularly true for Neuraminidase, for which the results at 0.1% of subsetting are either at 100% or 23% of recovered active depending on ligand query, 1A4G or 1INV ligands respectively.
Publication Year: 2009
Structural and functional basis of resistance to neuraminidase inhibitors of influenza B viruses.
(2010) J Med Chem 53
PubMed: 20695427 | PubMedCentral: PMC2932999 | DOI: 10.1021/jm100621s
The B/Perth D structure superimposes with a rmsd of 0.32 Å (over 388 Cα atoms) and 0.28 Å (over 385 Cα atoms) with B/Lee/40 (PDB 1INV) and B/Beijing/1/87 (PDB code 1NSB... ) NAs, respectively, illustrating the high degree of structural conservation in influenza B NAs.
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
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 Dihyd... ofolate 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
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