Improving the accuracy of predicting disulfide connectivity by feature selection

Journal of Computational Chemistry
Lin ZhuHong-Bin Shen

Abstract

Disulfide bonds are primary covalent cross-links formed between two cysteine residues in the same or different protein polypeptide chains, which play important roles in the folding and stability of proteins. However, computational prediction of disulfide connectivity directly from protein primary sequences is challenging due to the nonlocal nature of disulfide bonds in the context of sequences, and the number of possible disulfide patterns grows exponentially when the number of cysteine residues increases. In the previous studies, disulfide connectivity prediction was usually performed in high-dimensional feature space, which can cause a variety of problems in statistical learning, such as the dimension disaster, overfitting, and feature redundancy. In this study, we propose an efficient feature selection technique for analyzing the importance of each feature component. On the basis of this approach, we selected the most important features for predicting the connectivity pattern of intra-chain disulfide bonds. Our results have shown that the high-dimensional features contain redundant information, and the prediction performance can be further improved when these high-dimensional features are reduced to a lower but more compact ...Continue Reading

References

Jan 1, 1975·Advances in Protein Chemistry·C B Anfinsen, H A Scheraga
Jan 20, 1992·Journal of Molecular Biology·K C Chou
Jul 20, 1973·Science·C B Anfinsen
Sep 15, 1981·Journal of Molecular Biology·J M Thornton
Aug 6, 1999·Protein Engineering·M T PetersenS B Petersen
Oct 24, 2001·Bioinformatics·P Fariselli, R Casadio
Apr 2, 2002·Journal of Computational Chemistry·J L Klepeis, C A Floudas
Apr 6, 2002·Bioinformatics·Harpreet Kaur, G P S Raghava
Dec 31, 2003·Journal of Molecular Biology·Herman W T van VlijmenJuswinder Singh
Dec 4, 2004·Protein Engineering, Design & Selection : PEDS·Rajasri BhattacharyyaPinak Chakrabarti
Jun 28, 2005·Nucleic Acids Research·F Ferrè, P Clote
Sep 20, 2005·Proteins·Yu-Ching Chen, Jenn-Kang Hwang
Jul 18, 2006·Nucleic Acids Research·Alessio CeroniPaolo Frasconi
Feb 8, 2007·Proteins·Chih-Hao LuJenn-Kang Hwang
Apr 14, 2007·Current Protein & Peptide Science·Pawel SmialowskiDmitrij Frishman
Apr 21, 2007·Nature Protocols·Olof EmanuelssonHenrik Nielsen
Jun 23, 2007·Current Protein & Peptide Science·Chi-Hung TsaiJyh-Ping Hsu
Aug 19, 2007·IEEE Transactions on Nanobioscience·Ken-Li LinD Frank Hsu
Jan 22, 2008·Bioinformatics·Rotem Rubinstein, Andras Fiser
Feb 12, 2008·Journal of Proteome Research·Peilin JiaYudong Cai
Mar 29, 2008·Briefings in Functional Genomics & Proteomics·Rahul Singh
Aug 20, 2008·Bioinformatics·Tuo ZhangLukasz Kurgan
Aug 30, 2008·Journal of Computational Chemistry·Yingfu JiangLukasz Kurgan
Sep 19, 2008·Proteins·Andrew Kernytsky, Burkhard Rost
Jan 9, 2009·BMC Bioinformatics·Pengfei HanZhi-Ping Feng
Jan 28, 2009·Biochemical and Biophysical Research Communications·Liang LiuBing Niu

❮ Previous
Next ❯

Citations

May 25, 2011·Experimental Biology and Medicine·Vladimir L KolossovH Rex Gaskins
Apr 11, 2012·International Journal of Molecular Sciences·Xiaowei ZhaoMinghao Yin
Mar 5, 2013·Amino Acids·Dong-Jun YuJing-Yu Yang
Mar 11, 2015·International Journal of Molecular Sciences·Jingna SiRongling Wu
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Dong-Jun YuHong-Bin Shen
Oct 18, 2015·Computers in Biology and Medicine·Narjeskhatoon HabibiRazip Samian
May 12, 2015·TheScientificWorldJournal·Hao Lin, Wei Chen
Jan 1, 2013·Computational and Structural Biotechnology Journal·Antonin GuillouxJean-Luc Jestin
Dec 15, 2015·PloS One·Othman SoufanVladimir B Bajic
Dec 14, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Abdollah DehzangiTatsuhiko Tsunoda

❮ 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.