Citations in PubMed

Primary Citation PubMed: 1956054 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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


Dynamical basis for drug resistance of HIV-1 protease.

(2011) BMC Struct Biol 11

PubMed: 21740562 | PubMedCentral: PMC3149572 | DOI: 10.1186/1472-6807-11-31

Table 2 Clustering results of the ten bound forms PDB id Mutation RMSD (Å) Coupled with the active site Coupled with the flap region 2FNS 7 (substrate) Q7K, D25N, L63P, I64V 0.52 10 23 24 25 2... 27 28 29 30 31 84 85 86 87 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 1HPV 6 (Amprenavir) None 0.54 10 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 84 1HXB 6 (Saquinavir) None 0.31 10 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 84 1MUI 5 (Lopinavir) N37S 0.53 10 23 24 25 26 27 28 29 30 31 32 84 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 2O4K 8 (Atazanavir) Q7K 0.35 23 24 25 26 27 28 29 30 31 32 83 84 85 86 87 88 89 90 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 76 77 78 79 80 81 82 3JVY 6 (Darunavir) Q7K, L33I*, L63I, C67A, G86A, C95A 0.38 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84 2O4P 8 (Tipranavir) Q7K 0.39 23 24 25 26 27 28 29 30 31 32 83 84 85 86 87 88 89 90 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84 1HXW 6 (Ritonavir) None 0.40 10 23 24 25 26 27 28 29 30 31 85 86 87 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84 2PYN 6 (Nelfinavir) D30N, A71V* 0.26 10 23 24 25 26 27 28 29 30 31 32 84 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 2B7Z 7 (Indinavir) K20R*, V32I*, L33F*, M36I*, M46I*, L63P, A71V*,V82A*, I84V*, L90M* 0.32 10 22 23 24 25 26 27 28 29 84 85 86 34 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 76 77 78 79 80 81 82 83 The type of the ligand is listed in brackets.

Publication Year: 2011


In silico prediction of mutant HIV-1 proteases cleaving a target sequence.

(2014) PLoS One 9

PubMed: 24796579 | PubMedCentral: PMC4010418 | DOI: 10.1371/journal.pone.0095833

The starting structures were prepared from that of HIV-1 protease in complex with an inhibitor (PDB accession code 1HXB [40] ), considered as apo-protein.

Publication Year: 2014


Evaluation of novel Saquinavir analogs for resistance mutation compatibility and potential as an HIV-Protease inhibitor drug.

(2014) Bioinformation 10

PubMed: 24966525 | PubMedCentral: PMC4070054 | DOI: 10.6026/97320630010227

The bound form of HIV-1 PR subtype-B (PDB id: 1hxb) [ 19 ] using conformational dynamics studies with Saquinavir is reported to have resistant-mutation positions (10, 24 and 32) in the enzyme active s... te and positions (46, 47, 48, 50, 53, 54, 82 and 84) in the flap-region of the same protein.

Publication Year: 2014