Citations in PubMed

Primary Citation PubMed: 8590019 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

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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Computer-based screening of functional conformers of proteins.

(2008) PLoS Comput Biol 4

PubMed: 18463705 | PubMedCentral: PMC2265533 | DOI: 10.1371/journal.pcbi.1000009

For the HIV protease, 73 experimentally determined crystal structures were used: 1a30, 1a8g, 1a9m, 1aaq, 1ajv, 1ajx, 1axa, 1bdr, 1bv7, 1bv9, 1bwa, 1bwb, 1cpi, 1dif, 1dmp, 1gnm, 1gnn, 1gno, 1hbv, 1hih,... 1hiv, 1hos, 1hps, 1hpv, 1hpx, 1hsg, 1hte, 1htf, 1htg, 1hvc, 1hvi, 1hvj, 1hvk, 1hvl, 1hvr, 1hvs, 1hwr, 1hxb, 1hxw, 1mer, 1mes, 1met, 1meu, 1mtr, 1odw, 1odx, 1ody, 1ohr, 1pro, 1qbr, 1qbs, 1qbt, 1qbu, 1sbg, 1tcx, 1vij, 1vik, 1ytg, 1yth, 2aid, 2bpv, 2bpw, 2bpx, 2bpy, 2bpz, 2upj, 3aid, 4hvp, 4phv, 5hvp, 7hvp, 8hvp, 9hvp.

Publication Year: 2008


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


The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

(2011) J Biol Chem 286

PubMed: 21193411 | PubMedCentral: PMC3045013 | DOI: 10.1074/jbc.M110.178434

PDB codes of structural data of Hpx-1, Hpx-2, Hpx-9, and Hpx-13 used in this figure are 1SU3 , 1GEN , 1ITV , and 1HPX , respectively.

Publication Year: 2011


A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

(2008) Adv Appl Bioinform Chem 1

PubMed: 21918604 | PubMedCentral: PMC3169939 | DOI: null

Appendix A The protein databank (PDB) identifier list of the target protein set is: the PDB codes of COX2’s crystal structures are 1cx2, 1pxx, 4cox, 6cox, and 5cox; those of THR are 1tlp, 1tmn... 2tmn, and 1l3f; those of HIVP are 1aid, 1hpx, 1ivp, 1htf1, 1htf2, 4phv, and 3hvp; those of GST are 18gs, 2gss, 3pgt, and 16gs.

Publication Year: 2008


Rapid and accurate prediction and scoring of water molecules in protein binding sites.

(2012) PLoS One 7

PubMed: 22396746 | PubMedCentral: PMC3291545 | DOI: 10.1371/journal.pone.0032036

Protein PDB codes Resolution (Å) Ligand HIV-Protease 3FX5, 1HPX, 2ZYE a 0.93, 2,1.9 KNI-272 Ribonuclease A 1KF5, 1FS3, 5RSA a 1.2, 1.4, 2 None GluR2 ligand binding core 1FTM b , 1MY2 b 1.7, 1.... AMPA Trypsin 1S0Q, 1UTQ, 1TPO 1.0, 1.2, 1.7 None Concanavalin A 1NLS, 1GKB, 1JBC, 1QNY a 0.9, 1.6, 1.2, 1.8 None Glutathione S-transferase 1K3Y b , 1K3L b 1.3, 1,5 S-hexyl glutatione Carbonic Anhydrase 3KS3, 3MWO, 2ILI 0.9, 1.4, 1.1 None a Structures that have been determined by neutron diffraction.

Publication Year: 2012


Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking.

(2012) Pharmaceuticals (Basel) 5

PubMed: 24281339 | PubMedCentral: PMC3816669 | DOI: 10.3390/ph5121332

The target proteins were the macrophage migration inhibitory factor (PDB code: 1gcz), COX-2 (PDB code: 1cx2, 1pxx, 3pgh, 4cox and 6cox), HIV protease-1 (PDB code: 1aid, 1hpx and 1ivp), thermolysin (PD... code: 1tmn, 2tmn, 1tlp), and GST (PDB code: 18gs, 2gss, and 3pgt), and carboxypeptidase A (PDB code: 1cbx, 1cps, 3cpa).

Publication Year: 2012