Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 4

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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Computer-based screening of functional conformers of proteins.

(2008) PLoS Comput Biol 4

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

The PDB code of those structures in complex with a substrate analogue are: 1aaq, 1cpi, 1dmp, 1hbv, 1hih, 1hiv, 1hos, 1hps, 1hpv, 1hte, 1htf, 1htg, 1hvi, 1hvj, 1hvk, 1hvl, 1hvr, 1hvs, 1ohr, 1sbg, 2bpv,... 2bpw, 2bpx, 2bpy, 2bpz, 4hvp, 4phv, 5hvp, 7hvp, 8hvp, 9hvp.

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


Fpocket: an open source platform for ligand pocket detection.

(2009) BMC Bioinformatics 10

PubMed: 19486540 | PubMedCentral: PMC2700099 | DOI: 10.1186/1471-2105-10-168

Here the binding pocket of HIV1 protease is depicted in complex with the Dupont Merck inhibitor DMP450 (PDB code 1dmp ).

top right : Rank 1 pocket of the HIV1 Protease DMP450 complex (PDB Code: 1DMP ).

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