Primary Citation PubMed: 985462
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Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
(2007) Genome Biol 8
PubMed: 17335583 | PubMedCentral: PMC1868941 | DOI: 10.1186/gb-2007-8-3-r31
The α-carbon root mean square deviation (rmsd) between the X-ray structures (red) and reconstructed proteins (green) are 0.80 Å (1TIM-A) and 0.63 Å (1SYY-A), respectively.
Reconstructing protein A greedy algorithm and the evaluation criteria (global-fit score) presented by Kolodny and coworkers [ 15 ] were applied to measure the performance of 23-state structural alphabet (structural segments) in reconstructing the α-β-barrel protein (PDB code 1TIM-A [ 15 , 24 ]) and 38 structures (Additional data file 4) selected from the SCOP-516 set, which comprises 516 proteins.
Reconstruction of the (a) α-β-barrel protein (Protein Data Bank [PDB] code 1TIM-A ) and (b) ribonucleotide reductase (PDB code 1SYY-A ).
Publication Year: 2007
PMG: online generation of high-quality molecular pictures and storyboarded animations.
(2007) Nucleic Acids Res 35
PubMed: 17478496 | PubMedCentral: PMC1933120 | DOI: 10.1093/nar/gkm277
( B ) Simultaneous multiple representations: two chains isomerase (PDB code 1TIM).
Computer-based screening of functional conformers of proteins.
(2008) PLoS Comput Biol 4
PubMed: 18463705 | PubMedCentral: PMC2265533 | DOI: 10.1371/journal.pcbi.1000009
For every structure of the SCOP structural family 51351 (Triose Phosphate Isomerase family, including: 1TIM, 1AMK, 1CI1, 1HG3, 1M6J, 1B9B, 1TCD, 1TRE, 1YYA, 1HTI, 1R2R, 1MO0, 1YDV, 1YPI, 1WYI, 8TIM), ... e calculated their central residues.
Publication Year: 2008
Structure of triosephosphate isomerase from Cryptosporidium parvum.
(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67
PubMed: 21904056 | PubMedCentral: PMC3169408 | DOI: 10.1107/S1744309111019178
The first apo structure of TIM from chicken muscle was deposited in 1976 (PDB entry 1tim ; Banner et al. , 1976 ▶ ).
Publication Year: 2011
PubMed ID is not available.
Published in 2014
(C) Superimposed X-ray crystal structures of unliganded c TIM in the region of the N-terminal hinge: blue ribbon, wild-type c TIM (PDB entry 1TIM); green ribbon, unliganded L6RM of c TIM (PDB entry 4P... 1).
(E and F) Model for wild-type c TIM (PDB entry 1TIM), which shows, in red, the position in the protein structure where the binding of G3P results in significant values for δ NH (>0.1 ppm) for wild-type c TIM (E) or the L6RM (F).
(A) Wild-type c TIM (PDB entry 1TIM).
Publication Year: 2014
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