ArticleBMC structural biology2009
TIM-Finder: a new method for identifying TIM-barrel proteins.
Article in BMC structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins.BMC bioinformatics · 2019Article
- Recognition of Protein Pupylation Sites by Adopting Resampling Approach.Molecules (Basel, Switzerland) · 2018Article
- EPuL: An Enhanced Positive-Unlabeled Learning Algorithm for the Prediction of Pupylation Sites.Molecules (Basel, Switzerland) · 2017Article
- Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis.Biochimica et biophysica acta. General subjects · 2017Article
- Computational Prediction of RNA-Binding Proteins and Binding Sites.International journal of molecular sciences · 2015Review
- Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.PloS one · 2015Article
- Insights into the fold organization of TIM barrel from interaction energy based structure networks.PLoS computational biology · 2012Article
- Outer membrane proteins can be simply identified using secondary structure element alignment.BMC bioinformatics · 2011Article
- Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.PloS one · 2011Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsTo 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.
conclusionsTIM-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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