PMID: 9194156Apr 1, 1997Paper

Sequence-structure specificity--how does an inverse folding approach work?

Protein Engineering
W P HuJ Skolnick

Abstract

The inverse folding approach is a powerful tool in protein structure prediction when the native state of a sequence adopts one of the known protein folds. This is because some proteins show strong sequence-structure specificity in inverse folding experiments that allow gaps and insertions in the sequence-structure alignment. In those cases when structures similar to their native folds are included in the structure database, the z-scores (which measure the sequence-structure specificity) of these folds are well separated from those of other alternative structures. In this paper, we seek to understand the origin of this sequence-structure specificity and to identify how the specificity arises on passing from a short peptide chain to the entire protein sequence. To accomplish this objective, a simplified version of inverse folding, gapless inverse folding, is performed using sequence fragments of different sizes from 53 proteins. The results indicate that usually a significant portion of the entire protein sequence is necessary to show sequence-structure specificity, but there are regions in the sequence that begin to show this specificity at relatively short fragment size (15-20 residues). An island picture, in which the regions ...Continue Reading

Citations

Aug 22, 2001·Biopolymers·M R Betancourt, J Skolnick
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Y XuE C Uberbacher
Jan 29, 2000·Proteins·A KolinskiJ Skolnick

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