Citations in PubMed

Primary Citation PubMed: 7540935 Citations in PubMed

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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A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.

(2007) BMC Bioinformatics 8 Suppl 4

PubMed: 17570152 | PubMedCentral: PMC1892088 | DOI: 10.1186/1471-2105-8-S4-S9

(A) Immunoglobulin 48g7 germline fab (PDB id: 1AJ7 and 2RCS); (B) Adenylate kinase (PDB id: 1AKE and 4AKE); (C) HIV-1 reverse transcriptase (PDB id: 1VRT and 1RTJ); (D) Maltodextrin binding protein (P... B id: 1ANF and 1OMP).

Publication Year: 2007


Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

(2007) BMC Bioinformatics 8

PubMed: 17662112 | PubMedCentral: PMC2034607 | DOI: 10.1186/1471-2105-8-270

Blind heterodimer set a TS1, TS2 sets b PDB ID 20Cl Bastolla 6Cl PDB ID 20Cl Bastolla 6Cl 1ai7 1 1 1 1abr 4 2 3 1as4 1 1 1 1aui 1 1 1 1bpl 1 1 1 1ay7 3 3 2 1clv 2 1 2 1blx 3 6 3 1dj7 4 4 4 1c1y 3 4 3 ... dow 1 1 1 1dkf 2 47 1 1eud 8 9 7 1ugh 1 3 1 1f0c 1 1 1 1efv 1 1 1 1ksg 5 3 5 1ezq 1 1 1 1ku6 3 2 4 1f3v 67 145 36 1lot 1 1 1 1fle 19 4 9 1lpb 20 8 16 1hdm 1 1 1 1mhm 1 1 1 1itb 1 1 3 1mtp 1 1 1 1phn 1 1 1 1mzw 3 3 4 1qav 1 2 1 1npe 4 4 2 1smp 14 69 2 1nw9 1 10 1 1stf 2 5 1 1n52 10 1 9 D c 8/17 6/17 9/17 1o5m 3 1 2 D 3 13/17 9/17 15/17 1qge 1 1 1 1rke 1 1 1 1rtj 1 2 1 1ubt 1 2 1 4sgb 5 6 5 D c 13/24 13/24 13/24 D 3 17/24 18/24 16/24 Decoys constructed by other methods: Sternberg and Vakser decoys Limited series of protein–protein structures have been made available by Sternberg (ten series) and Vakser (five series) and coworkers, along with 99 high-quality decoys each.

Publication Year: 2007


HIV reverse transcriptase: structural interpretation of drug resistant genetic variants from India.

(2010) Bioinformation 4

PubMed: 20011151 | PubMedCentral: PMC2770369 | DOI: null

(B-F) Local hydrogen bond interactions involving K101 in unliganded RT structure 1DLO,1HMV,1RTD, 1RTJ and in Nevirapine bound RT 1VRT (G) Structural superposition of 1IKW (yellow) and 1RTJ (green) sho... ing changes in residue conformations.

In ligand unbound RT structure close to open conformation (1RTJ), Met 230 interacts with Trp 266 side chain through sulphur-π (pi) interaction ( Figure 2c ).

The protein databank codes of the crystal structures of bound and unbound forms of RT used in this study are 1IKW [ 6 ], 1VRT [ 7 ], 1DLO [ 8 ], 1HMV [ 9 ], 1RTJ [ 10 ] and 1RTD [ 11 ].

In the structure of RT (1RTJ), which largely corresponds to open conformation (Figure S1 in supplementary material ), Lys 101 forms a salt bridge with Glu 28.

(D)Changes due to K238T mutation (E) Comparison of side chain conformations of residues in the region involving Lys238, of Efavirenz bound RT, 1IKW (yellow) and of the unliganded form, 1RTJ (green) (F) Interactions involving K238 in Nevirapine bound RT (1VRT).

Figure 2 (A) Location of M230 (green) in Efavirenz (in orange) bound RT (1IKW) Interactions involving M230 in unliganded RT structures (B) 1DLO and (C) 1RTJ.

K101H ( Figure 1A ) shows the location of Lys 101 in the wild type unliganded RT crystal structure (1RTJ).

RT structure in the open conformation (1RTJ, green) superposed on Efavirenz bound RT (1IKW, yellow) is shown in Figure 3E .

(D) RT structure that corresponds to open conformation (1RTJ, green) superposed on Efavirenz (in orange) bound RT (1IKW, yellow) (E) Interactions involving M230 in Nevirapine bound RT (1VRT) (F) Model for M230L mutation.

Publication Year: 2010


Sequence and structure based models of HIV-1 protease and reverse transcriptase drug resistance.

(2013) BMC Genomics 14 Suppl 4

PubMed: 24268064 | PubMedCentral: PMC3849442 | DOI: 10.1186/1471-2164-14-S4-S3

Table 2 Sets of HIV-1 PR and RT residue positions used to construct feature vectors Set a Description Positions All EC scores at all residue positions in structures for HIV-1 PR (PDB ID: 3phv) and RT ... PDB ID: 1rtj, chain A) PIs: 1 - 99 NRTIs and NNRTIs: 1 - 543 IAS EC scores only at positions for which residue substitutions occur that are associated with drug resistance.

Computational mutagenesis methodology Structural coordinates for native HIV-1 PR and RT proteins were obtained from the Protein Data Bank (PDB accession codes: 3phv for PR; and 1rtj, chain A for RT) [ 26 ], which were used for generating residue-based coarse-grained representations of the proteins as collections of points in three-dimensional (3D) space, corresponding to centers of mass of the constituent amino acid residue side chains (Cα coordinates used for glycine).

Publication Year: 2013