Disulfide connectivity prediction with 70% accuracy using two-level models

Proteins
Bo-Juen ChenCheng-Yan Kao

Abstract

Disulfide bridges stabilize protein structures covalently and play an important role in protein folding. Predicting disulfide connectivity precisely helps towards the solution of protein structure prediction. Previous methods for disulfide connectivity prediction either infer the bonding potential of cysteine pairs or rank alternative disulfide bonding patterns. As a result, these methods encode data according to cysteine pairs (pair-wise) or disulfide bonding patterns (pattern-wise). However, using either encoding scheme alone cannot fully utilize the local and global information of proteins, so the accuracies of previous methods are limited. In this work, we propose a novel two-level framework to predict disulfide connectivity. With this framework, both the pair-wise and pattern-wise encoding schemes are considered. Our models were validated on the datasets derived from SWISS-PROT 39 and 43, and the results demonstrate that our models can combine both local and global information. Compared to previous methods, significant improvements were obtained by our models. Our work may also provide insights to further improvements of disulfide connectivity prediction and increase its applicability in protein structure analysis and pred...Continue Reading

References

Aug 1, 1990·Protein Engineering·S M MuskalS H Kim
Dec 9, 1994·Journal of Molecular Biology·P M Harrison, M J Sternberg
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Apr 12, 2000·Biochemistry·W J WedemeyerH A Scheraga
Oct 24, 2001·Bioinformatics·P Fariselli, R Casadio
Oct 17, 2002·Protein Science : a Publication of the Protein Society·Pier Luigi MartelliRita Casadio
Dec 31, 2003·Journal of Molecular Biology·Herman W T van VlijmenJuswinder Singh
Sep 30, 2004·Protein Science : a Publication of the Protein Society·Pier Luigi MartelliRita Casadio
Sep 20, 2005·Proteins·Yu-Ching Chen, Jenn-Kang Hwang

❮ Previous
Next ❯

Citations

Jan 22, 2008·Bioinformatics·Rotem Rubinstein, Andras Fiser
Jan 16, 2008·BMC Bioinformatics·Marc VincentPaolo Frasconi
Feb 4, 2010·Journal of Computational Chemistry·Lin ZhuHong-Bin Shen
Jan 16, 2014·IEEE Transactions on Nanobioscience·William Murad, Rahul Singh
Nov 3, 2015·Evolutionary Bioinformatics Online·Alfonso E Márquez-Chamorro, Jesús S Aguilar-Ruiz
Aug 31, 2010·Science China. Chemistry·Chen YanyiYang Jenny Jie
Nov 23, 2006·Molecular Biology and Evolution·Jianzhi Zhang

❮ 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.