title: A modular kernel approach for integrative analysis of protein domain boundaries.
abstract: BACKGROUND
  In this paper, we introduce a novel inter-range interaction integrated approach for protein domain boundary prediction. It involves (1) the design of modular kernel algorithm, which is able to effectively exploit the information of non-local interactions in amino acids, and (2) the development of a novel profile that can provide suitable information to the algorithm. One of the key features of this profiling technique is the use of multiple structural alignments of remote homologues to create an extended sequence profile and combines the structural information with suitable chemical information that plays an important role in protein stability. This profile can capture the sequence characteristics of an entire structural superfamily and extend a range of profiles generated from sequence similarity alone.
  
  
  RESULTS
  Our novel profile that combines homology information with hydrophobicity from SARAH1 scale was successful in providing more structural and chemical information. In addition, the modular approach adopted in our algorithm proved to be effective in capturing information from non-local interactions. Our approach achieved 82.1%, 50.9% and 31.5% accuracies for one-domain, two-domain, and three- and more domain proteins respectively.
  
  
  CONCLUSIONS
  The experimental results in this study are encouraging, however, more work is need to extend it to a broader range of applications. We are currently developing a novel interactive (human in the loop) profiling that can provide information from more distantly related homology. This approach will further enhance the current study.
authors: Advanced Networks Research Group, School of Information Technologies (J12), the University of Sydney, NSW 2006, Australia. dyoo4334@it.usyd.edu.au
authors: Paul D
authors: PD
authors: Yoo
authors: Bing Bing
authors: BB
authors: Zhou
authors: Albert Y
authors: AY
authors: Zomaya
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins