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[…] tory Animals, the Guide for the Care and Use of Laboratory Animals, and the Division of Comparative Medicine, Washington University School of Medicine. All animal work was approved under WUSM Institutional Animal Care and Use Protocol 20120025., Kinase domain models were downloaded from the Kinomer website (http://www.compbio.dundee.ac.uk/kinomer/allPK.hmm) and were used to screen a collection of gene sets from the organisms Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Meloidogyne incognita, Saccharomyces cerevisiae, and Trichinella spiralis. Custom score thresholds per kinase group were taken from Miranda-Saavedra and then adjusted until an hmmpfam search (HMMER v2.3.2) came as close as possible to identifying all known C.elegans kinases using the Kinomer allPK.hmm profile database. Those same cutoffs were then applied to the gene sets of the remaining 6 organisms, identifying sets of putative kinases in each case. These putative kinases were categorized into the 8 conventional kinase groups (ePK) and the 4 atypical kinase groups (aPK) by merit of which model they were found to hit in the Kinomer profile database (allPK.hmm)., We then manually curated the sets of putative kinases by screening them against Pfam using hmmpfam (as a part of an interproscan run (interproscan software v4.5, interpro db release 2.2)) and making sure that no clear contradictions were found. Any cases where a putatively identified kinase was found to have a clearly non-kinase Pfam domain hit, were removed from the final set of identifications. The custom cutoffs used per kinase group were as follows: TK, 5.5e-03; CAMK, 9.6e-07; CK1, 1.1e-02; CMGC, 6.7e-03; AGC, 1.1e-14; STE, 3.4e-03; RGC, 4.8e-05; TKL, 8.7e-03; PDHK, 4.7e-160; PIKK, 1.4e-06; Alpha, 8.5e-66; RIO, 7.5e-10., The same methodology used to classify the nematode kinases was also used to classify targets in DrugBank. DrugBank v2.5 was used to screen against the kinase domain models using an E-value cutoff of 0.1. If the target in DrugBank […]

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