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. 2004 Jul 1;32(Web Server issue):W64-8.
doi: 10.1093/nar/gkh451.

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences

Dmitry A Afonnikov  1 , Nikolay A Kolchanov
Affiliations

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences

Dmitry A Afonnikov et al. Nucleic Acids Res. .

Abstract

Recent results suggest that during evolution certain substitutions at protein sites may occur in a coordinated manner due to interactions between amino acid residues. Information on these coordinated substitutions may be useful for analysis of protein structure and function. CRASP is an Internet-available software tool for the detection and analysis of coordinated substitutions in multiple alignments of protein sequences. The approach is based on estimation of the correlation coefficient between the values of a physicochemical parameter at a pair of positions of sequence alignment. The program enables the user to detect and analyze pairwise relationships between amino acid substitutions at protein sequence positions, estimate the contribution of the coordinated substitutions to the evolutionary invariance or variability in integral protein physicochemical characteristics such as the net charge of protein residues and hydrophobic core volume. The CRASP program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/.

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Figures

Figure 1
Figure 1
(A) A schematic representation of coordinated substitutions in a pair of amino acid residues forming a salt-bridge in a putative protein. (B) Proteins that contain residues of the same charge at positions 4 and 7 are unstable and are eliminated during evolution; in contrast, those containing residues of different charges are stable and can occur in multiple sequence alignments.
Figure 2
Figure 2
The program package CRASP. The three main modules for analysis of coordinated substitutions accept multiple sequence alignments and enable the estimation of (A) pairwise covariation between the physicochemical property values at protein positions, (B) analysis of dependencies at specific position pairs and (C) the contribution of covarying substitutions to the invariance or variability in integral physicochemical characteristics.
See this image and copyright information in PMC

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