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FOR THE RECORD

Structural interpretation of mutations and SNPs using STRAP-NT

Institute of Biochemistry Charité, Medical Faculty of the Humboldt University, 10117 Berlin, Germany

(RECEIVED October 5, 2005; FINAL REVISION October 12, 2005; ACCEPTED October 13, 2005)

Visualization of residue positions in protein alignments and mapping onto suitable structural models is an important first step in the interpretation of mutations or polymorphisms in terms of protein function, interaction, and thermodynamic stability. Selecting and highlighting large numbers of residue positions in a protein structure can be time-consuming and tedious with currently available software. Previously, a series of tasks and analyses had to be performed one-by-one to map mutations onto 3D protein structures; STRAP-NT is an extension of STRAP that automates these tasks so that users can quickly and conveniently map mutations onto 3D protein structures. When the structure of the protein of interest is not yet available, a related protein can frequently be found in the structure databases. In this case the alignment of both proteins becomes the crucial part of the analysis. Therefore we embedded these program modules into the Java-based multiple sequence alignment program STRAP-NT. STRAP-NT can simultaneously map an arbitrary number of mutations denoted using either the nucleotide or amino acid sequence. When the designations of the mutations refer to genomic sites, STRAP-NT translates them into the corresponding amino acid positions, taking intron–exon boundaries into account. STRAP-NT tightly integrates a number of current protein structure viewers (currently PYMOL, RASMOL, JMOL, and VMD) with which mutations and polymorphisms can be directly displayed on the 3D protein structure model. STRAP-NT is available at the PDB site and at http://www.charite.de/bioinf/strap/ or http://strapjava.de.

Keywords: protein structure/folding; 3D structure; genotype/phenotype relationship; structure visualization; mutation screening; mutations/SNPs

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051882006.

Reprint requests to: Christoph Gille, Institute of Biochemistry Charité, Medical Faculty of the Humboldt University, 10117 Berlin, Monbijoustrasse 2, Germany; e-mail: christoph.gille{at}charite.de; fax: +49-30-450528942.

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