Classification of C2H2 Zinc Finger Domains Using Support Vector Machines

نویسندگان

  • Takafumi Nagano
  • Makiko Suwa
  • Kiyoshi Asai
چکیده

Zinc finger proteins include nuclear receptors for steroid hormones and are mainly DNA-binding transcription factors. Thus those are supposed to be target proteins for drug discovery. C2H2 zinc finger gene family is one of the most popular and complex superfamilies. C2H2 zinc finger domains are composed of approximately 25 to 30 amino acid residues including the paired cysteines and histidines that form coordinate bonds with zinc ion. Although C2H2 domains are well-studied, it is difficult to detect the domains with high accuracy by means of homology search or hidden Markov models(HMMs) owing to a wide variety of the sequences. In this research, we have extended the Support Vector Machine(SVM) based method using the Fisher kernel [1] in order to achieve better accuracy than an HMM. The Fisher kernel extracts a fixed length vector of features known as a Fisher score vector (FSV) from a variable length sequence with an HMM. The method in [1] classifies G-protein coupled receptors (GPCRs) into GPCR subfamilies.

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تاریخ انتشار 2002