ArticleBMC bioinformatics2007
Flexible mapping of homology onto structure with homolmapper.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2.The New phytologist · 2017Article
- Identification of the Plant Ribokinase and Discovery of a Role for Arabidopsis Ribokinase in Nucleoside Metabolism.The Journal of biological chemistry · 2016Article
- Structure of the GH76 α-mannanase homolog, BT2949, from the gut symbiont Bacteroides thetaiotaomicron.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Hooking She3p onto She2p for myosin-mediated cytoplasmic mRNA transport.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The ebolavirus VP24 interferon antagonist: know your enemy.Virulence · 2012Article
- The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold.PLoS pathogens · 2012Article
- Structural and mechanistic insight into N-glycan processing by endo-α-mannosidase.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- VENN, a tool for titrating sequence conservation onto protein structures.Nucleic acids research · 2009Article
- Structural and functional analysis of SmeT, the repressor of the Stenotrophomonas maltophilia multidrug efflux pump SmeDEF.The Journal of biological chemistry · 2009Article
- Coevolution in defining the functional specificity.Proteins · 2009Article
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2 authors.
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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 http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm.
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