Prediction of protein local structures and folding fragments based on building-block library

Proteins
Qi-wen DongLei Lin

Abstract

In recent years, protein structure prediction using local structure information has made great progress. In this study, a novel and effective method is developed to predict the local structure and the folding fragments of proteins. First, the proteins with known structures are split into fragments. Second, these fragments, represented by dihedrals, are clustered to produce the building blocks (BBs). Third, an efficient machine learning method is used to predict the local structures of proteins from sequence profiles. Finally, a bi-gram model, trained by an iterated algorithm, is introduced to simulate the interactions of these BBs. For test proteins, the building-block lattice is constructed, which contains all the folding fragments of the proteins. The local structures and the optimal fragments are then obtained by the dynamic programming algorithm. The experiment is performed on a subset of the PDB database with sequence identity less than 25%. The results show that the performance of the method is better than the method that uses only sequence information. When multiple paths are returned, the average classification accuracy of local structures is 72.27% and the average prediction accuracy of local structures is 67.72%, whic...Continue Reading

References

Jul 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·A M Lesk, G D Rose
Nov 4, 1994·Journal of Molecular Biology·S Henikoff, J G Henikoff
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 12, 1998·Journal of Molecular Biology·C Bystroff, D Baker
Mar 24, 1999·Trends in Biochemical Sciences·R L Baldwin, G D Rose
Mar 31, 1999·Trends in Biochemical Sciences·R L Baldwin, G D Rose
Dec 14, 1999·Nature Structural Biology·M LlinásS Marqusee
Jun 14, 2000·Journal of Molecular Biology·Y I WolfE V Koonin
Aug 5, 2000·Journal of Molecular Biology·C BystroffD Baker
Aug 10, 2002·Bioinformatics·Christopher Bystroff, Yu Shao
Oct 17, 2002·Journal of Molecular Biology·Rachel KolodnyMichael Levitt
Feb 11, 2003·Proteins·Cornelius G Hunter, Shankar Subramaniam
May 23, 2003·Protein Science : a Publication of the Protein Society·Nurit HaspelRuth Nussinov
Jul 2, 2003·Bioinformatics·An-Suei Yang, Lu-yong Wang
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Nov 25, 2003·Bioinformatics·Yuna HouChristopher Bystroff
Apr 23, 2004·Proteins·Rachel KarchinKevin Karplus
May 19, 2004·Journal of Molecular Biology·A C CamprouxP Tufféry
May 21, 2004·Protein Science : a Publication of the Protein Society·J Bradley Holmes, Jerry Tsai
Jun 25, 2004·Nucleic Acids Research·Frédéric GuyonPierre Tufféry
Sep 24, 2004·Proteins·Yuna HouChristopher Bystroff
Mar 9, 2005·Biophysical Chemistry·Julian LeeJooyoung Lee
Apr 12, 2005·Proteins·Catherine EtchebestAlexandre G de Brevern
Nov 23, 2005·Bioinformatics·Jean-Christophe GellySerge Hazout
Dec 24, 2005·Proteins·Vladimir Yarov-YarovoyDavid Baker
Dec 31, 2005·Nucleic Acids Research·Andrei KouranovHelen M Berman
Jan 13, 2006·BMC Bioinformatics·Oliver SanderThomas Lengauer
Jul 18, 2006·Nucleic Acids Research·J-C GellyA G de Brevern
Aug 4, 2006·Nucleic Acids Research·Jinn-Moon Yang, Chi-Hua Tung
Nov 14, 2006·Journal of Molecular Biology·Hidenori KatoYawen Bai
Dec 15, 2006·BMC Structural Biology·Juliette MartinFrançois Rodolphe
Jan 25, 2007·Journal of Bioinformatics and Computational Biology·Ching-Tai ChenWen-Lian Hsu
May 12, 2007·Computers in Biology and Medicine·Qi-wen DongLei Lin
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

❮ Previous
Next ❯

Citations

Jul 24, 2010·RNA·Samuel Coulbourn Flores, Russ B Altman
Feb 22, 2011·Journal of Theoretical Biology·Alexandre G de Brevern, Agnel Praveen Joseph
Jul 25, 2009·Computational Biology and Chemistry·Manoj TyagiAlexandre G de Brevern
Nov 4, 2015·Computational and Mathematical Methods in Medicine·Zhiqiang ZengZhiling Hong

❮ 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.