Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods

Bioinformatics
Hong SuJianyi Yang

Abstract

The interactions between protein and nucleic acids play a key role in various biological processes. Accurate recognition of the residues that bind nucleic acids can facilitate the study of uncharacterized protein-nucleic acids interactions. The accuracy of existing nucleic acids-binding residues prediction methods is relatively low. In this work, we introduce NucBind, a novel method for the prediction of nucleic acids-binding residues. NucBind combines the predictions from a support vector machine-based ab-initio method SVMnuc and a template-based method COACH-D. SVMnuc was trained with features from three complementary sequence profiles. COACH-D predicts the binding residues based on homologous templates identified from a nucleic acids-binding library. The proposed methods were assessed and compared with other peering methods on three benchmark datasets. Experimental results show that NucBind consistently outperforms other state-of-the-art methods. Though with higher accuracy, similar to many other ab-initio methods, cross prediction between DNA and RNA-binding residues was also observed in SVMnuc and NucBind. We attribute the success of NucBind to two folds. The first is the utilization of improved features extracted from thr...Continue Reading

References

Jan 1, 1984·Annual Review of Biochemistry·P H von HippelJ A McSwiggen
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 22, 2005·BMC Bioinformatics·Shandar Ahmad, Akinori Sarai
Jul 18, 2006·Nucleic Acids Research·Liangjiang Wang, Susan J Brown
May 8, 2007·Nucleic Acids Research·Michael TerribiliniDrena Dobbs
Oct 13, 2007·Proteins·Manish KumarG P S Raghava
Jun 28, 2011·BMC Systems Biology·Jingna SiBingding Huang
Oct 25, 2011·Journal of Structural Biology·Tomasz PutonJanusz M Bujnicki
Dec 27, 2011·Nature Methods·Michael RemmertJohannes Söding
Jul 23, 2013·Molecular BioSystems·Huiying ZhaoYaoqi Zhou
Dec 31, 2014·Nature Methods·Jianyi YangYang Zhang
Jun 26, 2015·Nucleic Acids Research·Zhenling Peng, Lukasz Kurgan
Dec 19, 2015·PLoS Computational Biology·Zhichao Miao, Eric Westhof
Oct 28, 2016·Methods in Molecular Biology·Zhenling PengLukasz Kurgan
May 19, 2017·Nucleic Acids Research·Yumeng YanSheng-You Huang

❮ Previous
Next ❯

Citations

Sep 24, 2020·International Journal of Molecular Sciences·Kui WangLukasz Kurgan
Oct 30, 2020·Nucleic Acids Research·Bi ZhaoLukasz Kurgan
Aug 21, 2021·Briefings in Bioinformatics·Jian ZhangLukasz Kurgan
Dec 21, 2021·Briefings in Bioinformatics·Junkang WeiYu Li
Jan 19, 2022·Briefings in Bioinformatics·Qianmu YuanYuedong Yang

❮ 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.