Citations in PubMed

Primary Citation PubMed: 1304383 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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Improved prediction of critical residues for protein function based on network and phylogenetic analyses.

(2005) BMC Bioinformatics 6

PubMed: 16124876 | PubMedCentral: PMC1208857 | DOI: 10.1186/1471-2105-6-213

The Protein Data Bank (PDB) files used for each of these three proteins are respectively 1BTL, 1HIV and 2LZM [[ 13 , 14 ] and [ 15 ]].

Phylogenetic approaches Protein sequences from 2LZM, 1BTL, 1HIV, 1GVP, 1A2P and the set of 128 PDB proteins were aligned with their homologues using the Conseq server [ 18 ] or using the alignments provided for these three proteins in the Hssp database [ 22 , 23 ].

The parameters used to run the Conseq server for 2LZM, 1BTL and 1HIV were: Maximum likelihood method used to calculate the conservation scores, PSI-BLAST E-value = 0.001, maximum number of homologous sequences = 50 and the number of PSI-BLAST iterations = l (except for 2LZM, for which it was 3).

Publication Year: 2005


Wiggle-predicting functionally flexible regions from primary sequence.

(2006) PLoS Comput Biol 2

PubMed: 16839194 | PubMedCentral: PMC1500818 | DOI: 10.1371/journal.pcbi.0020090

(D) Structural mapping of FF score with gradient from negative (blue) to positive (red), (PDB ID: 1HIV).

Publication Year: 2006


Efficient identification of critical residues based only on protein structure by network analysis.

(2007) PLoS One 2

PubMed: 17502913 | PubMedCentral: PMC1855080 | DOI: 10.1371/journal.pone.0000421

Briefly, the T4L-HIV-TEM1 set includes three enzymes that have been extensively characterized structurally and functionally (TEM1 beta-lactamase (PDB code 1BTL), HIV-1 protease (PDB code 1HIV) and T4 ... ysozyme (PDB code 2LZM)).

Publication Year: 2007


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.

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.

Publication Year: 2008


Integration of open access literature into the RCSB Protein Data Bank using BioLit.

(2010) BMC Bioinformatics 11

PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220

Two example URLs are given to demonstrate the communication process: The first URL allows access to BioLit information for all articles containing a particular PDB ID: http://biolit.ucsd.edu/ws/rest/a... ticles/pdbid/1HIV/metadata (to request articles for PDB ID 1HIV).

Publication Year: 2010