A structural study for the optimisation of functional motifs encoded in protein sequences.

ABSTRACT:

Background

A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that--at least in some cases--the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure.

Results

Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues s

SUBMITTER: Via A 

PROVIDER: S-EPMC420233 | biostudies-literature | 2004 Apr

REPOSITORIES: biostudies-literature