Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices

Details Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices

2007-11-07

arxiv.org/abs/0711.1010v1

PLoS ONE, 3:e1963 (2008)

Biology

Quantitative Biology

Biomolecules

22 pages, 7 figures, 4 tables

Scientific paper

10.1371/journal.pone.0001963

Position-specific scoring matrices (PSSMs) are useful for detecting weak homology in protein sequence analysis, and they are thought to contain some essential signatures of the protein families. In order to elucidate what kind of ingredients constitute such family-specific signatures, we apply singular value decomposition to a set of PSSMs and examine the properties of dominant right and left singular vectors. The first right singular vectors were correlated with various amino acid indices including relative mutability, amino acid composition in protein interior, hydropathy, or turn propensity, depending on proteins. A significant correlation between the first left singular vector and a measure of site conservation was observed. It is shown that the contribution of the first singular component to the PSSMs act to disfavor potentially but falsely functionally important residues at conserved sites. The second right singular vectors were highly correlated with hydrophobicity scales, and the corresponding left singular vectors with contact numbers of protein structures. It is suggested that sequence alignment with a PSSM is essentially equivalent to threading supplemented with functional information. The presented method may be used to separate functionally important sites from structurally important ones, and thus it may be a useful tool for predicting protein functions.

Affiliated with

Also associated with

No associations

Rating

Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-502006