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Paper   IPM / Computer Science / 10936
School of Computer Science
  Title:   olvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix
  Author(s): 
1.  H. Goodarzi
2.  A. Katanforoush
3.  N. Torabid
4.  H. Shateri Najafabadi
  Status:   Published
  Journal: Journal of Theoretical Biology
  No.:  4
  Vol.:  245
  Year:  2007
  Pages:   715-725
  Supported by:  IPM
  Abstract:
Cost measure matrices or different amino acid indices have been widely used for studies in many fields of biology. One major criticism of these studies might be based on the unavailability of an unbiased and yet effective amino acid substitution matrix. Throughout this study we have devised a cost measure matrix based on the solvent accessibility, residue charge, and residue volume indices. Performed analyses on this novel substitution matrix (i.e. solvent accessibility charge volume (SCV) matrix) support the uncontaminated nature of this matrix regarding the genetic code. Although highly similar to a number of previously available cost measure matrices, the SCV matrix results in a more significant optimality in the error-buffering capacity of the genetic code when compared to many other amino acid substitution matrices. Besides, a method to compare an SCV-based scoring matrix with a number of widely used matrices has been devised, the results of which highlights the robustness of this matrix in protein family discrimination.

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