Prediction of protein subcellular locations by GO-FunD-PseAA predictor

Biochemical and Biophysical Research Communications
Kuo-Chen Chou, Yu-Dong Cai

Abstract

The localization of a protein in a cell is closely correlated with its biological function. With the explosion of protein sequences entering into DataBanks, it is highly desired to develop an automated method that can fast identify their subcellular location. This will expedite the annotation process, providing timely useful information for both basic research and industrial application. In view of this, a powerful predictor has been developed by hybridizing the gene ontology approach [Nat. Genet. 25 (2000) 25], functional domain composition approach [J. Biol. Chem. 277 (2002) 45765], and the pseudo-amino acid composition approach [Proteins Struct. Funct. Genet. 43 (2001) 246; Erratum: ibid. 44 (2001) 60]. As a showcase, the recently constructed dataset [Bioinformatics 19 (2003) 1656] was used for demonstration. The dataset contains 7589 proteins classified into 12 subcellular locations: chloroplast, cytoplasmic, cytoskeleton, endoplasmic reticulum, extracellular, Golgi apparatus, lysosomal, mitochondrial, nuclear, peroxisomal, plasma membrane, and vacuolar. The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an...Continue Reading

References

Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·K C Chou, C T Zhang
Jan 1, 1997·Nucleic Acids Research·A Bairoch, R Apweiler
Feb 28, 1997·Journal of Molecular Biology·J CedanoE Querol
Jun 1, 1997·Current Opinion in Structural Biology·M G ClarosG von Heijne
Jun 20, 1998·Nucleic Acids Research·A Reinhardt, T Hubbard
Nov 14, 1998·Biochemical and Biophysical Research Communications·K C Chou, D W Elrod
Feb 13, 1999·Journal of Protein Chemistry·G P Zhou
Apr 9, 1999·Protein Engineering·K C Chou, D W Elrod
Jul 13, 2000·Journal of Molecular Biology·O EmanuelssonG von Heijne
Mar 17, 2001·International Journal of Biological Macromolecules·Z P Feng, C T Zhang
May 17, 2001·Proteins·G P Zhou, N Assa-Munt
Aug 21, 2002·The Journal of Biological Chemistry·Kuo-Chen Chou, Yu-Dong Cai
Dec 10, 2002·Proteins·Guo-Ping Zhou, Kutbuddin Doctor
Nov 19, 2003·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Yu-Dong Cai

❮ Previous
Next ❯

Citations

Jan 5, 2008·Amino Acids·Loris Nanni, Alessandra Lumini
Aug 23, 2008·Amino Acids·Xiaoqi ZhengJun Wang
Jan 25, 2007·Journal of Bioinformatics and Computational Biology·Jian GuoHoward Leung
Feb 3, 2011·BMC Bioinformatics·Suyu MeiShuigeng Zhou
Aug 21, 2007·BMC Bioinformatics·Serene A K OngZhiwei Cao
Nov 29, 2008·BMC Bioinformatics·Aarti Garg, Gajendra P S Raghava
Jul 28, 2013·SpringerPlus·Faezeh HosseinzadehBahram Goliaei
Jul 18, 2006·Biochemical and Biophysical Research Communications·Yan WangJin Xu
May 29, 2012·Journal of Proteomics·Xianping FangSonglin Ruan
Dec 21, 2010·Journal of Theoretical Biology·Kuo-Chen Chou
Sep 22, 2010·Biochemical and Biophysical Research Communications·Wei Chen, Hao Lin
Aug 4, 2010·Biochemical and Biophysical Research Communications·Sang-Mun Chi
Nov 15, 2008·Analytical Biochemistry·Hong-Bin Shen, Kuo-Chen Chou
Aug 19, 2007·Analytical Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
Apr 13, 2007·Biochemical and Biophysical Research Communications·Peilin JiaYixue Li
Nov 17, 2010·Proteomics·Yie Hou LeeMaxey C M Chung
Sep 17, 2004·Biochemical and Biophysical Research Communications·Yu-Dong Cai, Kuo-Chen Chou
Jul 26, 2015·Journal of Theoretical Biology·Abdulaziz Yousef, Nasrollah Moghadam Charkari

❮ 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.