Protein molecular function annotation methods can incorporate evolutionary information, such as the phylogenic tree shown here, to improve their performance. This figure represents the predictions of one such method, SIFTER, for proteins in the adenosine-5-monophosphate/adenosine deaminase family, including confidence values for the predicted functional annotations (see Engelhardt et al).
Image Credit: Designed by Steven Chan (http://www.stevenchan.us). Created in Blender (http://www.blender.org) and composited in Adobe Photoshop. Phylogeny image by ATV, created by C. Zmasek (http://www.phylogenomics.us/atv)
Editorial
Ten Simple Rules for Getting Published
PLOS Computational Biology: published October 28, 2005 | https://doi.org/10.1371/journal.pcbi.0010057
Message from ISCB
The ISCB: Growing and Evolving in Step with Science
PLOS Computational Biology: published October 28, 2005 | https://doi.org/10.1371/journal.pcbi.0010051
Research Articles
Protein Molecular Function Prediction by Bayesian Phylogenomics
PLOS Computational Biology: published October 7, 2005 | https://doi.org/10.1371/journal.pcbi.0010045
Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs
PLOS Computational Biology: published October 14, 2005 | https://doi.org/10.1371/journal.pcbi.0010046
Structural Evolution of the Protein Kinase–Like Superfamily
PLOS Computational Biology: published October 21, 2005 | https://doi.org/10.1371/journal.pcbi.0010049
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
PLOS Computational Biology: published October 28, 2005 | https://doi.org/10.1371/journal.pcbi.0010053
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction
PLOS Computational Biology: published October 28, 2005 | https://doi.org/10.1371/journal.pcbi.0010054
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
PLOS Computational Biology: published October 28, 2005 | https://doi.org/10.1371/journal.pcbi.0010055