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PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

(2011) J Chem Inf Model 51

PubMed: 21728306 | PubMedCentral: PMC3180202 | DOI: 10.1021/ci200082t

Table 2 Congeneric Series Present in the Data Set protein count ligand series type pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id HIV-1 protease (L63P) 11 hydroxyethylami... e 2cem 2cen 2qnq 1g2k 1d4i 1d4j 1ebz 1ec0 1ec1 1ec2 1xl5 HIV-1 protease (WT) 11 hydroxyethylamine 2psv 2q54 2qhy 2qhz 2qi1 2qi3 2qi4 2qi5 2qi6 2i0a 2i0d tyrosine-protein phosphatase 8 thiophene-dicarboxylic acid 2hb1 2qbq 2qbr 2qbs 2zmm 2zn7 2azr 2b07       coagulation factor X 6 pyrrolidin-2-one 2uwl 2uwp 2cji 2j2u 2j34 2j4i           carbonic anhydrase 2 6 sulfamide analogues 2h15 2pov 2pow 3bl0 2hd6 2pou           tRNA guanine transglycosylase 5 quinazolin-4-one 2bbf 1r5y 1s38 1s39 1q4w             HMGCoA reductase 5 atorvastatin analogues 3ccw 3ccz 3cd7 3cd0 3cda             acetylcholinesterase 4 huperzine/hupyridone 1vot 1gpk 1h22 1h23               estrogen receptor alpha 4 phenol 2pog 2r6w 2ayr 1qkt               urokinase 4 benzamidine analogues 1gja 1gj8 1gjd 1gi9               β-1,4-xylanase 3 aza-sugar analogues 1fh8 1fh9 1fhd                 glutamate [NMDA] receptor ζ1 3 small ring amino carboxylic acid 1y1m 1y1z 1y20                 lectin 3 saccharides 1ax1 1ax0 1ax2                 membrane lipoprotein tmpC 3 purine neucloside analogues 2fqw 2fqx 2fqy                 retropepsin 3 macrocyclic peptidomimetic 1b6j 1b6l 1b6m                 transporter (LeuT) 3 small amino acid 3f3d 3f48 3f4j                 The range of affinities in the CSAR-NRC set is quite large, 14 orders of magnitude in p K d .

Publication Year: 2011

Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.

(2009) Acta Pharmacol Sin 30

PubMed: 19935678 | PubMedCentral: PMC4007494 | DOI: 10.1038/aps.2009.159

Target PDB entries a Number of Actives b ACE 1UZF, 1O86, 1UZE * 14 AChE 1ACJ, 1ACL, 1AMN, 1AX9, 1DX6, 1E3Q, 1E66, 1EVE, 1GPK, 1GPN, 1GQR, 1GQS, 1H22, 1H23, 1HBJ, 1JJB, 1OCE, 1ODC, 1U65, 1UT6, ... VOT, 1W4L, 1W6R, 1W76, 1ZGC, 2ACE, 2ACK * , 2BAG, 2C4H, 2C5F, 2C5G, 2C58, 2CEK, 2CKM, 2CMF, 2J3Q, 2VB4 22 AR 1E3G * , 1GS4, 1T5Z, 1T63, 1T65, 1XJ7, 1XOW, 1XQ3, 1Z95, 2AM9, 2AMA, 2AMB, 2AO6, 2AX6, 2AX7, 2AX8, 2AX9, 2AXA, 2HVC, 2OZ7, 2PIO, 2PIP, 2PIQ, 2PIR, 2PIT, 2PIU, 2PIV, 2PIW, 2PIX, 2PKL, 2PNU, 2Q7I, 2Q7J, 2Q7K, 2Q7L, 2Z4J 16 DacA 1CEF, 1CEG * , 1HVB, 1IKG, 1IKI, 1MPL, 1PW1, 1PW8, 1PWC, 1PWD, 1PWG, 1SCW, 1SDE, 1YQS 3 DHFR 1BOZ * , 1KMS, 1KMV, 1S3U, 1S3V, 1S3W, 2DHF, 1DLS, 1U72, 1MVS, 1MVT, 1DLR, 1U71, 1HFP, 1HFQ, 1HFR, 1OHJ, 1OHK, 1DHF, 1DRF, 1PD8, 1PD9 8 ERα 1A52, 1AKF, 1ERE, 1ERR, 1G50, 1GWQ, 1GWR, 1L2I, 1PCG * , 1QKT, 1R5K, 1UOM, 1X7E, 1X7R, 1XP1, 1XP6, 1XP9, 1XPC, 1YIM, 1ZKY, 2AYR, 2B1V, 2B1Z, 2BJ4, 2FAI, 2G44, 2G5O, 2I0J, 2IOG, 2JF9, 2JFA, 2OUZ, 2P15, 2POG, 2Q6J, 2Q70, 2QE4, 3ERD, 3ERT 32 HIV-pr 1AID, 1HVH, 1HVR, 1HWR, 1IZH, 1IZI, 1JLD, 1KZK, 1NPV, 1NPW, 1T3R, 1T7K, 1TCX, 1XL2, 1XL5, 1YT9, 2A4F * , 2AID, 2F3K, 2FDD, 2FDE, 2FGU, 2FGV, 2HC0, 2NXD, 2NXM, 2P3A, 2P3B, 2P3C, 2P3D, 3AID, 4PHV 9 TK 1E2I, 1E2J, 1E2K * , 1E2L, 1E2M, 1E2N, 1E2P, 1KI2, 1KI3, 1KI4, 1KI6, 1KI7, 1KI8, 1KIM, 1OF1, 1P7C, 1QHI, 1VTK, 2KI5, 2VTK, 3VTK 8 a All the X-ray crystal structures of the complexes of each target in complex with ligands were used in the construction of pharmacophore models.

Publication Year: 2009