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Literature DB >> 16267083

SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles.

Abstract

MOTIVATION: The prediction of protein domains is a crucial task for functional classification, homology-based structure prediction and structural genomics. In this paper, we present the SSEP-Domain protein domain prediction approach, which is based on the application of secondary structure element alignment (SSEA) and profile-profile alignment (PPA) in combination with InterPro pattern searches. SSEA allows rapid screening for potential domain regions while PPA provides us with the necessary specificity for selecting significant hits. The combination with InterPro patterns allows finding domain regions without solved structural templates if sequence family definitions exist.
RESULTS: A preliminary version of SSEP-Domain was ranked among the top-performing domain prediction servers in the CASP 6 and CAFASP 4 experiments. Evaluation of the final version shows further improvement over these results together with a significant speed-up. AVAILABILITY: The server is available at http://www.bio.ifi.lmu.de/SSEP/

Entities: Gene

Mesh：

Substances：
Proteins

Year: 2005 PMID： 16267083 DOI： 10.1093/bioinformatics/bti751

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

19 in total

1. DomSVR: domain boundary prediction with support vector regression from sequence information alone.

Authors: Peng Chen; Chunmei Liu; Legand Burge; Jinyan Li; Mahmood Mohammad; William Southerland; Clay Gloster; Bing Wang
Journal: Amino Acids Date: 2010-02-18 Impact factor: 3.520

2. Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps.

Authors: Sajid Mahmud; Zhiye Guo; Farhan Quadir; Jian Liu; Jianlin Cheng
Journal: BMC Bioinformatics Date: 2022-07-19 Impact factor: 3.307

3. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Authors: Eshel Faraggi; Yuedong Yang; Shesheng Zhang; Yaoqi Zhou
Journal: Structure Date: 2009-11-11 Impact factor: 5.006

SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles.

1. DomSVR: domain boundary prediction with support vector regression from sequence information alone.

2. Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps.

3. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

4. OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries.

5. The MULTICOM toolbox for protein structure prediction.

6. Prediction of protein domain with mRMR feature selection and analysis.

7. Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics.

8. ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.

9. DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy.

10. The effect of edge definition of complex networks on protein structure identification.