Citations in PubMed

Primary Citation PubMed: 9554878 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces.

(2009) Bioinformatics 25

PubMed: 19179356 | PubMedCentral: PMC2654803 | DOI: 10.1093/bioinformatics/btp058

This pattern also occurs in the obligate interactions between chain A and B of 1CWQ, between chain A and B of 1E0P and between chain A and B of 6UPJ; and in the transient interaction between chain A a... d B of PDB 1HVH.

Publication Year: 2009


A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction.

(2010) BMC Bioinformatics 11

PubMed: 20398404 | PubMedCentral: PMC2868011 | DOI: 10.1186/1471-2105-11-193

Table 1 PDB codes of the protein-ligand complexes in the three test sets HIV protease complexes ( N = 112) 1GNM , 1GNN , 1GNO , 1A30 , 1A9M , 1AAQ , 1AJV , 1AJX , 1B6J , 1B6K , 1B6L , 1B6M , 1BDQ , 1B... 7 , 1BV9 , 1BWA , 1BWB , 1C70 , 1D4K , 1D4L , 1D4Y , 1DIF , 1DMP , 1G2K , 1G35 , 1HBV , 1HEG , 1HIH , 1HII , 1HOS , 1HPO , 1HPS , 1HPV , 1HPX , 1HSH , 1HVH , 1HVI , 1HVJ , 1HVK , 1HVL , 1HVR , 1HVS , 1HWR , 1HXB , 1HXW , 1IIQ , 1IZH , 1IZI , 1LZQ , 1MES , 1MET , 1MEU , 1MRW , 1MRX , 1MSM , 1MSN , 1MTR , 1NH0 , 1ODY , 1OHR , 1PRO , 1QBR , 1QBS , 1QBT , 1QBU , 1SBG , 1SDT , 1SDU , 1SDV , 1SGU , 1SH9 , 1T7J , 1W5V , 1W5W , 1W5X , 1W5Y , 1Z1H , 1Z1R , 1ZP8 , 1ZPA , 1ZSF , 1ZSR , 2AOC , 2AOD , 2AOE , 2AQU , 2AVM , 2AVO , 2AVQ , 2AVS , 2AVV , 2BPV , 2BPY , 2BQV , 2F80 , 2F81 , 2F8G , 2FGU , 2FGV , 2HB3 , 2I0A , 2I0D , 7HVP , 7UPJ , 2HS2 , 2AOG , 2HS1 , 1A94 , 1AID , 1KZK , 1TCX , 3AID Trypsin complexes ( N = 73) 1C1R , 1C5P , 1C5Q , 1C5S , 1C5T , 1CE5 , 1F0T , 1F0U , 1K1I , 1K1J , 1K1L , 1K1M , 1K1N , 1OSS , 1PPC , 1PPH , 1QB1 , 1QB6 , 1QB9 , 1QBN , 1QBO , 1TNG , 1TNH , 1TNI , 1TNJ , 1TNK , 1TNL , 1V2J , 1V2K , 1V2L , 1V2N , 1V2Q , 1V2R , 1V2S , 1V2T , 1V2U , 1V2W , 2A31 , 2BZA , 2FX6 , 1BRA , 1G3B , 1G3C , 1G3D , 1G3E , 1GHZ , 1GI1 , 1GI4 , 1GI6 , 1GJ6 , 1J16 , 1J17 , 1O2H , 1O2J , 1O2K , 1O2N , 1O2O , 1O2Q , 1O2S , 1O2W , 1O2X , 1O2Z , 1O30 , 1O33 , 1O36 , 1O38 , 1O3D , 1O3F , 1O3H , 1O3I , 1O3J , 1O3K , 1V2O Carbonic anhydrase complexes ( N = 44) 1BN1 , 1BN3 , 1BN4 , 1BNN , 1BNQ , 1BNT , 1BNU , 1BNV , 1BNW , 1A42 , 1AVN , 1BCD , 1CIL , 1CIM , 1CIN , 1CNW , 1CNX , 1CNY , 1G1D , 1G45 , 1G46 , 1G48 , 1G4J , 1G4O , 1G52 , 1G53 , 1G54 , 1I9L , 1I9M , 1I9N , 1I9O , 1I9P , 1I9Q , 1IF7 , 1IF8 , 1OKL , 1TTM , 1XPZ , 1XQ0 , 1YDA , 1YDB , 1YDD , 2EZ7 , 2H4N In addition, a set of putative binding poses were prepared for the ligand molecule in each complex in all three test sets.

Publication Year: 2010


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

Variation of the parameter lambda corresponds to a continuous deformation of the HIV-1 protease receptor structure beginning at the bound form pdb ID 1HVH (lambda = 1) and following th... order 1DMP, 1HWR, 2UPJ, 1AJV, 1G2K and ending with 7UPJ (lambda = 7) which represent a minimum RMSD protein pathway.

The seven selected HIV-1 protease structures were extracted from pdb-files 1AJV, 1DMP, 1G2K, 1HVH, 1HWR, 2UPJ, and 7UPJ crystallized in the presence of different ligands each representing a different binding site structure (conformational changes are illustrated in Figure 1 ).

Publication Year: 2012


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