Flexible mapping of homology onto structure with Homolmapper

We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs.Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at http:/ / www.mcb.ucdavis.edu/ faculty-labs/ lagarias/ homolmapper_home/ homolmapper%20web%20page.htm webcite.The proliferation of known or suspected protein sequences in the post-genomic era and the slower, but steady, progress in protein structure determination implies that there are a large number of proteins with no experimentally determined structure but with varying homology to a protein of known structure. When such proteins are of experimental or practical interest, several approaches can be used to generate some form of approximate structural information to aid in the design or interpretation of biochemical experiments. For example, homology modeling can be used to build a model structure for the protein of interest based on the known structure. First introduced in 1969 [1], homology modeling has become a more commonly applied tool in recent years. However, homology modeling remains sensitive not only to the multiple sequence alignment (MSA) of h