A quadratic approximation for protein sequence to structure mapping

  • Authors:

  • SeYoung Oh;Jae Heon Yun;Sei-Young Chung

  • Affiliations:

  • Department of Mathematics, Chungnam National University, Daejeon 305-764, Korea;Department of Mathematics, College of Natural Sciences, Chungbuk National University, Cheongju 361-763, Korea;Department of Mathematics, Chungnam National University, Daejeon 305-764, Korea

  • Venue:
  • The Korean Journal of Computational & Applied Mathematics
  • Year:
  • 2003

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Abstract

A method is proposed to predict the distances between given residue pairs (between Cα atoms) of a protein using a sequence to structure mapping by indefinite quadratic approximation The prediction technique requires a data fitting in three dimensional space with coordinates of the residues of known structured proteins and leads to a numerical representation of 20 amino acids by minimizing a large least norm iteratively. These approximations are used in distance prediction for given residue pairs. Some computational experience on a test set of small proteins from Brookhaven Protein Data Bank are given.