Prediction of phosphorylation sites using SVMs

Bioinformatics
Jong Hun KimInsong Koh

Abstract

Phosphorylation is involved in diverse signal transduction pathways. By predicting phosphorylation sites and their kinases from primary protein sequences, we can obtain much valuable information that can form the basis for further research. Using support vector machines, we attempted to predict phosphorylation sites and the type of kinase that acts at each site. Our prediction system was limited to phosphorylation sites catalyzed by four protein kinase families and four protein kinase groups. The accuracy of the predictions ranged from 83 to 95% at the kinase family level, and 76-91% at the kinase group level. The prediction system used-PredPhospho-can be applied to the functional study of proteins, and can help predict the changes in phosphorylation sites caused by amino acid variations at intra- and interspecies levels.

Citations

May 5, 2012·Amino Acids·Dariusz PlewczynskiIndrajit Saha
Jan 8, 2008·Science in China. Series C, Life Sciences·MingHui WangCunXin Wang
Jan 6, 2010·ACS Chemical Biology·Paul A GrimsrudJoshua J Coon
Aug 8, 2009·The Journal of Biological Chemistry·Hueng-Chuen FanPeter A McNaughton
Aug 13, 2010·Molecular & Cellular Proteomics : MCP·Jianjiong GaoDong Xu
May 9, 2008·Molecular & Cellular Proteomics : MCP·Yu XueXuebiao Yao
Feb 25, 2005·Bioinformatics·Dariusz PlewczynskiLeszek Rychlewski
Aug 12, 2008·Bioinformatics·Chia-Ying YangChi-Ying F Huang
Oct 23, 2008·Bioinformatics·Thanh Hai DangKris Laukens
Sep 9, 2009·Bioinformatics·Babak BostanPaul Lu
Sep 20, 2011·Bioinformatics·Brett Trost, Anthony Kusalik
Jul 18, 2006·Nucleic Acids Research·Yu XueXuebiao Yao
Jul 18, 2006·Nucleic Acids Research·Hu ChenZhirong Sun
Dec 5, 2006·Nucleic Acids Research·Andreas ZanzoniManuela Helmer-Citterich
Nov 6, 2007·Nucleic Acids Research·Rune LindingTony Pawson
Aug 15, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Brian A JoughinMichael B Yaffe
Apr 29, 2010·BMC Bioinformatics·Subhadip Basu, Dariusz Plewczynski
Jan 19, 2011·BMC Bioinformatics·Jianjiong Gao, Dong Xu
Nov 13, 2007·BMC Bioinformatics·Cornelia CarageaVasant Honavar
Mar 28, 2008·BMC Structural Biology·James KitchenJim Warwicker
Dec 15, 2011·Proteome Science·Javad SafaeiSteven Pelech

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.