title: TIM-Finder: a new method for identifying TIM-barrel proteins.
abstract: 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/.
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China. sijingna@gmail.com
authors.forename: Jing-Na
authors.initials: JN
authors.lastname: Si
authors.forename: Ren-Xiang
authors.initials: RX
authors.lastname: Yan
authors.forename: Chuan
authors.initials: C
authors.lastname: Wang
authors.forename: Ziding
authors.initials: Z
authors.lastname: Zhang
authors.forename: Xiao-Dong
authors.initials: XD
authors.lastname: Su
mesh_terms: 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
chemical_list: D007527:Isoenzymes; D020543:Proteome; D014305:Triose-Phosphate Isomerase