iNR-PhysChem: a sequence-based predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix.

PloS One
Xuan XiaoKuo-Chen Chou

Abstract

Nuclear receptors (NRs) form a family of ligand-activated transcription factors that regulate a wide variety of biological processes, such as homeostasis, reproduction, development, and metabolism. Human genome contains 48 genes encoding NRs. These receptors have become one of the most important targets for therapeutic drug development. According to their different action mechanisms or functions, NRs have been classified into seven subfamilies. With the avalanche of protein sequences generated in the postgenomic age, we are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what subfamily it belongs to? To address these problems, we developed a predictor called iNR-PhysChem in which the protein samples were expressed by a novel mode of pseudo amino acid composition (PseAAC) whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross-covariance transformations. It was observed that the overall success rate achieved by iNR-PhysChem was over 98% in identifying NRs or non-NRs, and over 92% in identifying NRs among the following seven subfamilies: NR1--thyroid hormone like, NR2--HNF4-like, NR...Continue Reading

References

Jan 1, 1986·Journal of Biochemistry·H NakashimaT Ooi
Jun 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·T P Hopp, K R Woods
Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·K C Chou, C T Zhang
Dec 15, 1995·Cell·D J MangelsdorfR M Evans
Dec 10, 1998·Nucleic Acids Research·S KawashimaM Kanehisa
Feb 13, 1999·Journal of Protein Chemistry·G P Zhou
Apr 9, 1999·Protein Engineering·K C Chou, D W Elrod
Apr 29, 1999·Cell·UNKNOWN Nuclear Receptors Nomenclature Committee
Jul 16, 1999·Steroids·R Kumar, E B Thompson
May 17, 2001·Proteins·G P Zhou, N Assa-Munt
Jun 22, 2001·The Journal of Biological Chemistry·C ChangT Kodadek
Jul 19, 2001·The Journal of Biological Chemistry·J M Olefsky
Nov 10, 2001·Trends in Endocrinology and Metabolism : TEM·L Altucci, H Gronemeyer
Jan 30, 2002·Molecular and Biochemical Parasitology·Kirsten CrossgroveClaude V Maina
Aug 21, 2002·The Journal of Biological Chemistry·Kuo-Chen Chou, Yu-Dong Cai
Sep 5, 2002·Nature Reviews. Molecular Cell Biology·Jamshed R Tata
Dec 10, 2002·Proteins·Guo-Ping Zhou, Kutbuddin Doctor
Jan 23, 2003·Journal of Cell Science·Marc Robinson-RechaviVincent Laudet
Mar 25, 2004·The Journal of Biological Chemistry·Manoj Bhasin, Gajendra P S Raghava
Dec 9, 2004·Current Drug Targets. Inflammation and Allergy·Natalia Novac, Thorsten Heinzel
Jul 29, 2006·Computational Biology and Chemistry·Kanaka Durga KedarisettiScott Dick
Aug 19, 2007·Analytical Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
Nov 3, 2007·Analytical Biochemistry·Hong-Bin Shen, Kuo-Chen Chou
Nov 14, 2007·Nucleic Acids Research·Shuichi KawashimaMinoru Kanehisa
Dec 17, 2008·Protein and Peptide Letters·Guang-Ya ZhangBai-Shan Fang

❮ Previous
Next ❯

Citations

Mar 22, 2014·International Journal of Molecular Sciences·Yue-Nong FanKuo-Chen Chou
Jan 29, 2014·International Journal of Molecular Sciences·Wang-Ren QiuKuo-Chen Chou
May 8, 2014·BioMed Research International·Pengmian FengYongchun Zuo
Jan 13, 2015·International Journal of Proteomics·Arvind Kumar Tiwari, Rajeev Srivastava
Jun 22, 2012·PloS One·Bi-Qing LiKuo-Chen Chou
Apr 5, 2016·Computer Methods and Programs in Biomedicine·Muhammad Iqbal, Maqsood Hayat
Nov 17, 2012·Journal of Theoretical Biology·Chenglong YuStephen S-T Yau
Dec 4, 2015·BMC Bioinformatics·Hongchu Wang, Xuehai Hu
Aug 11, 2015·Computational Biology and Chemistry·Arvind Kumar Tiwari, Rajeev Srivastava
Aug 2, 2015·Journal of Theoretical Biology·Soheila ShokrollahzadeSamad Jahandideh
Jun 27, 2014·BioMed Research International·Wei ChenKuo-Chen Chou
Dec 29, 2013·BioMed Research International·Jian-Liang MinKuo-Chen Chou
Mar 28, 2017·BMC Bioinformatics·Prabina Kumar MeherAtmakuri Ramakrishna Rao
Nov 30, 2019·Current Pharmaceutical Design·Kuo-Chen Chou
Oct 29, 2021·Biopolymers·Hongliang ZouZhijian Yin
Mar 31, 2019·Journal of Biomedical Informatics·Kanica Sachdev, Manoj Kumar Gupta

❮ Previous
Next ❯

Software Mentioned

LIBSVM
2L
iNR
PseAAC
PhysChem
NR
BLAST

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.