Prediction of lipid-binding sites based on support vector machine and position specific scoring matrix.

The Protein Journal
Wenjia XiongMenglong Li

Abstract

Lipid-protein interactions play a vital role in various biological processes, which are involved in cellular functions and can affect the stability, folding and the function of peptides and proteins. In this study, a sequence-based method by using support vector machine and position specific scoring matrix (PSSM) was proposed to predict lipid-binding sites. Considering the influence of surrounding residues of one amino acid, a sliding window was chosen to encode the PSSM profiles. By incorporating the evolutionary information and the local features of residues surrounding one lipid-binding site, the method yielded a high accuracy of 80.86% and the Matthew's Correlation Coefficient of 0.58 by using fivefold cross validation test. The good result indicates the applicability of the method.

References

Oct 20, 1975·Biochimica Et Biophysica Acta·B W Matthews
Jan 1, 1997·Annual Review of Nutrition·D A BernlohrL J Banaszak
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 10, 2001·Current Opinion in Structural Biology·E Pebay-Peyroula, J P Rosenbusch
Oct 9, 2001·Trends in Biochemical Sciences·V Niggli
Apr 2, 2002·Journal of Computational Chemistry·Yu-Dong CaiKuo-Chen Chou
Aug 21, 2002·The Journal of Biological Chemistry·Kuo-Chen Chou, Yu-Dong Cai
Feb 20, 2003·Protein Science : a Publication of the Protein Society·Harpreet Kaur, Gajendra Pal Singh Raghava
Jul 16, 2003·Peptides·Yu-Dong CaiKuo-Chen Chou
Feb 22, 2005·BMC Bioinformatics·Shandar Ahmad, Akinori Sarai
Aug 16, 2005·Prostaglandins & Other Lipid Mediators·Daniele Piomelli
Aug 16, 2005·Prostaglandins & Other Lipid Mediators·Richard W GrossXianlin Han
Mar 30, 2006·Theoretical Biology & Medical Modelling·David L ScottWolfgang H Goldmann
Oct 13, 2007·Arteriosclerosis, Thrombosis, and Vascular Biology·Christopher J LelliottDaniel Lindén
Oct 13, 2007·Proteins·Manish KumarG P S Raghava
May 23, 2008·Current Opinion in Structural Biology·Carola Hunte, Sebastian Richers
Jan 1, 2008·International Journal of Computational Biology and Drug Design·Liangjiang WangJack Y Yang
Jul 19, 2006·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Heather E Findlay, Paula J Booth

❮ Previous
Next ❯

Citations

Nov 14, 2013·Chemistry and Physics of Lipids·Michael D Best
Nov 8, 2015·Bioinformatics·Yusuke KomiyamaKentaro Shimizu
May 14, 2014·Journal of Theoretical Biology·Mohammad Reza BakhtiarizadehEsmaeil Ebrahimie
Mar 12, 2015·Journal of Chemical Information and Modeling·Nan LiuLeslie A Kuhn

❮ 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.