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Protein threading using PROSPECT: Design and evaluation by Ying Xu; Dong Xu is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Protein threading using PROSPECT: Design and evaluation about?

The computer system PROSPECT for the protein fold recognition using the threading method is described and evaluated in this article. For a given target protein sequence and a template structure, PROSPECT guarantees to find a globally optimal threading alignment between the two. The scoring function for a threading alignment employed in PROSPECT consists of four additive terms: i) a mutation term, ii) a singleton fitness term, iii) a pairwise-contact potential term, and iv) alignment gap penalties. The current version of PROSPECT considers pair contacts only between core (␣-helix or ␤-strand) residues and alignment gaps only in loop regions. PROSPECT finds a globally optimal threading efficiently when pairwise contacts are considered only between residues that are spatially close (7 Å or less between the C ␤ atoms in the current implementation). On a test set consisting of 137 pairs of target-template proteins, each pair being from the same superfamily and having sequence identity < 30%, PROSPECT recognizes 69% of the templates correctly and aligns 66% of the structurally alignable residues correctly. These numbers may be compared with the 55% fold recognition and 64% alignment accu

Who reads Protein threading using PROSPECT: Design and evaluation?

Author

Ying Xu; Dong Xu

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2000

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)