Flexible mapping of homology onto structure with Homolmapper

Nathan C Rockwell,J Clark Lagarias

doi:10.1186/1471-2105-8-123

Nathan C Rockwell, J Clark Lagarias

Open Access

https://doi.org/10.1186/1471-2105-8-123

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Journal: BMC bioinformatics	Publication Date: Apr 11, 2007
Citations: 68	License type: CC BY 2.0

Affiliation: University of California, Davis

Abstract

BackgroundOver the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine.ResultsWe 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.ConclusionHomolmapper 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 .

Highlights

Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context
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
Homology modeling remains sensitive to the multiple sequence alignment (MSA) of homologous proteins, and to the particular algorithms used in the structural modeling [2]

Summary

Introduction

A number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. 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. The confidence assigned to such models is dependent on the (page number not for citation purposes)

Results

Discussion

Conclusion