Knowledge-based three-body potential for transcription factor binding site prediction

IET Systems Biology
Wenyi QinHui Lu

Abstract

A structure-based statistical potential is developed for transcription factor binding site (TFBS) prediction. Besides the direct contact between amino acids from TFs and DNA bases, the authors also considered the influence of the neighbouring base. This three-body potential showed better discriminate powers than the two-body potential. They validate the performance of the potential in TFBS identification, binding energy prediction and binding mutation prediction.

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Apr 12, 2002·Proceedings of the National Academy of Sciences of the United States of America·Edo KussellEugene I Shakhnovich
Mar 9, 2004·Journal of Molecular Biology·M Michael GromihaAkinori Sarai
Apr 2, 2005·Journal of Medicinal Chemistry·Chi ZhangYaoqi Zhou
Oct 26, 2005·Nucleic Acids Research·Alexandre V MorozovEric D Siggia
Jan 30, 2007·Nucleic Acids Research·Jason E DonaldEugene I Shakhnovich
Nov 16, 2007·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Guijun ZhaoHui Lu
Jun 3, 2008·Nucleic Acids Research·Mu Gao, Jeffrey Skolnick
Oct 17, 2008·BMC Bioinformatics·Vladimir Espinosa AngaricaBruno Contreras-Moreira
Feb 9, 2012·PloS One·Chien-Yu ChenDarby Tien-Hao Chang
Jul 17, 2012·Current Opinion in Structural Biology·Limin Angela Liu, Philip Bradley
Aug 28, 2012·Nucleic Acids Research·Mark Maienschein-ClineFangping Mu
Oct 9, 2012·Proteins·Mohammed AlQuraishi, Harley H McAdams
Dec 12, 2012·Bioinformatics·Takako TakedaJun-Tao Guo
Dec 19, 2012·BMC Bioinformatics·Chih Lee, Chun-Hsi Huang

❮ Previous
Next ❯

Citations

Apr 6, 2019·Database : the Journal of Biological Databases and Curation·Oscar FranzénJohan L M Björkegren
Jul 31, 2019·Annals of the New York Academy of Sciences·Khai Li Chai, Merrole Cole-Sinclair

❮ 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.

Related Papers

Future Medicinal Chemistry
Karen T Schomburg, Matthias Rarey
Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Guijun ZhaoHui Lu
© 2021 Meta ULC. All rights reserved