Predicting kinase substrates using conservation of local motif density
نویسندگان
چکیده
منابع مشابه
Predicting kinase substrates using conservation of local motif density
MOTIVATION Protein kinases represent critical links in cell signaling. A central problem in computational biology is to systematically identify their substrates. RESULTS This study introduces a new method to predict kinase substrates by extracting evolutionary information from multiple sequence alignments in a manner that is tolerant to degenerate motif positioning. Given a known consensus, t...
متن کاملPredicting the Density of Algae Communities using Local Regression Trees
This paper describes the application of local regression trees to an environmental regression task. This task was part of the 3 Internation ERUDIT Competition. The technique described in this paper was announced as one of the three runner-up methods by the jury of the competition. We briefly describe RT, a system that is able to generate local regression trees. We emphasise the multi-strategy f...
متن کاملPredicting CK2 beta-dependent substrates using linear patterns
CK2 is a constitutively active Ser/Thr protein kinase deregulated in cancer and other pathologies, responsible for about the 20% of the human phosphoproteome. The holoenzyme is a complex composed of two catalytic (α or α´) and two regulatory (β) subunits, with individual subunits also coexisting in the cell. In the holoenzyme, CK2β is a substrate-dependent modulator of kinase activity. Therefor...
متن کاملPredicting Negative CouchSurfing Experiences using Local Information
We attempt to predict negative references in the CouchSurfing (CS) social network using an SVM classifier. The low frequency of negative references, however, makes prediction very difficult. We attempt to achieve a classifier with a high F1 score by training on data sets with varying distributions of positive and negative examples and by manipulating the decision boundary. We also explore how t...
متن کاملStudies on the specificity of phosphorylase kinase using peptide substrates.
The action of phosphorylase kinase on synthetic peptides is reported. These peptides are variants of the amino acid sequence. Ser-Asp-Gln-Glu-Lys-Arg-Lys-Gln-Ile-Ser-Val-Arg-Gly-Leu, found in the natural substrate, phosphorylase b. The effects of size, the cluster of basic groups at the NH2-terminal side, the phosphorylatable seryl residue, the hydrophobic groups surrounding serine, and the arg...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2012
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/bts060