DOMpro

DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Protein domains are the structural and functional units of proteins. The ability to parse protein chains into different domains is important for protein classification and for understanding protein structure, function, and evolution. Here we use machine learning algorithms, in the form of recursive neural networks, to develop a protein domain predictor called DOMpro. DOMpro predicts protein domains using a combination of evolutionary information in the form of profiles, predicted secondary structure, and predicted relative solvent accessibility. DOMpro is trained and tested on a curated dataset derived from the CATH database. DOMpro correctly predicts the number of domains for 69% of the combined dataset of single and multi-domain chains. DOMpro achieves a sensitivity of 76% and specificity of 85% with respect to the single-domain proteins and sensitivity of 59% and specificity of 38% with respect to the two-domain proteins. DOMpro also achieved a sensitivity and specificity of 71% and 71% respectively in the Critical Assessment of Fully Automated Structure Prediction 4 (CAFASP-4) (Fisher et al., 1999; Saini and Fischer, 2005) and was ranked among the top ab initio domain predictors. The DOMpro server, software, and dataset are available at http://www.igb.uci.edu/servers/psss.html.


References in zbMATH (referenced in 4 articles )

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  1. Hajij, Mustafa; Jonoska, NataĊĦa; Kukushkin, Denys; Saito, Masahico: Graph based analysis for gene segment organization in a scrambled genome (2020)
  2. Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei: A topological approach for protein classification (2015)
  3. Elloumi, Mourad (ed.); Zomaya, Albert Y. (ed.): Algorithms in computational molecular biology. Techniques approaches and applications. (2011)
  4. Cheng, Jianlin; Sweredoski, Michael J.; Baldi, Pierre: DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks (2006) ioport