Prediction of Nitrated Tyrosine Residues in Protein Sequences by Extreme Learning Machine and Feature Selection Methods

Combinatorial Chemistry & High Throughput Screening
Lei ChenYudong Cai

Abstract

Accurately recognizing nitrated tyrosine residues from protein sequences would pave a way for understanding the mechanism of nitration and the screening of the tyrosine residues in sequences. In this study, we proposed a prediction model that used the extreme learning machine (ELM) algorithm as the prediction engine to identify nitrated tyrosine residues. To encode each tyrosine residue, a sliding window technique was adopted to extract a peptide segment for each tyrosine residue, from which a number of features were extracted. These features were analyzed by a popular feature selection method, Minimum Redundancy Maximum Relevance (mRMR) method, producing a feature list, in which all features were ranked in a rigorous way. Then, the Incremental Feature Selection (IFS) method was utilized to discover the optimal features, on which the optimal ELM-based prediction model was built. This model produced satisfactory results on the training dataset with a Matthews correlation coefficient of 0.757. The model was also evaluated by an independent test dataset that contained only positive samples, yielding a sensitivity of 0.938. Compared to other prediction models that use classic machine learning algorithms as prediction engines on the...Continue Reading

Citations

Feb 13, 2019·Combinatorial Chemistry & High Throughput Screening·Tianyun WangXian Zhao
Nov 6, 2018·International Journal of Molecular Sciences·Lei ChenYu-Dong Cai
Dec 28, 2018·Combinatorial Chemistry & High Throughput Screening·ShaoPeng WangYudong Cai
Oct 17, 2018·Journal of Clinical Medicine·Yu-Dong CaiXiangyin Kong
Aug 10, 2019·BioMed Research International·Fei YuanYu-Dong Cai
Sep 5, 2019·International Journal of Molecular Sciences·Lei ChenYu-Dong Cai
Jan 31, 2019·Combinatorial Chemistry & High Throughput Screening·Yunhua ZhangLijuan Chen

❮ 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.