Primary Citation PubMed: 1304383
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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
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