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,...

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Bibliographic Details
Published in:BMC structural biology Vol. 9; no. 1; p. 73
Main Authors: Si, Jing-Na, Yan, Ren-Xiang, Wang, Chuan, Zhang, Ziding, Su, Xiao-Dong
Format: Journal Article
Language:English
Published: London BioMed Central 14.12.2009
BioMed Central Ltd
Subjects:
Amino Acid Motifs
Bacillus subtilis - chemistry
Biochemistry
Bioinformatics
Biomedical and Life Sciences
Colleges & universities
Computational Biology - methods
Crystallography and Scattering Methods
Databases, Nucleic Acid
Genetic algorithms
Identification systems
Isoenzymes - analysis
Isoenzymes - chemistry
Isoenzymes - metabolism
Life Sciences
Mass Spectrometry
Methodology Article
Methods
Models, Molecular
Physiological aspects
Programming languages
Protein Folding
Protein Science
Protein Structure, Secondary
Protein Structure, Tertiary
Proteins
Proteome - analysis
Proteome - chemistry
Proteome - metabolism
Sequence Analysis, Protein
Spectroscopy/Spectrometry
Structure
Triose-Phosphate Isomerase - analysis
Triose-Phosphate Isomerase - chemistry
Triose-Phosphate Isomerase - metabolism
Triosephosphate isomerase
Support Vector Machine Model
Query Sequence
Support Vector Machine
Triosephosphate Isomerase
Protein Pair
ISSN:1472-6807, 1472-6807
Online Access:Get full text
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Summary: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/ .
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ISSN:1472-6807
1472-6807
DOI:10.1186/1472-6807-9-73