TIM-Finder: a new method for identifying TIM-barrel proteins.
BACKGROUND
The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.


RESULTS
To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.


CONCLUSIONS
TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/.
Si
Jing-Na
JN
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China. sijingna@gmail.com
Yan
Ren-Xiang
RX
Wang
Chuan
C
Zhang
Ziding
Z
Su
Xiao-Dong
XD
D020816:Amino Acid Motifs; D001412:Bacillus subtilis / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D007527:Isoenzymes / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D020539:Sequence Analysis, Protein; D014305:Triose-Phosphate Isomerase / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism
D007527:Isoenzymes; D020543:Proteome; D014305:Triose-Phosphate Isomerase