Remote homolog detection using local sequence-structure correlations

Proteins
Yuna HouChristopher Bystroff

Abstract

Remote homology detection refers to the detection of structural homology in proteins when there is little or no sequence similarity. In this article, we present a remote homolog detection method called SVM-HMMSTR that overcomes the reliance on detectable sequence similarity by transforming the sequences into strings of hidden Markov states that represent local folding motif patterns. These state strings are transformed into fixed-dimension feature vectors for input to a support vector machine. Two sets of features are defined: an order-independent feature set that captures the amino acid and local structure composition; and an order-dependent feature set that captures the sequential ordering of the local structures. Tests using the Structural Classification of Proteins (SCOP) 1.53 data set show that the SVM-HMMSTR gives a significant improvement over several current methods.

References

Jan 1, 1990·Methods in Enzymology·W R Pearson
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jul 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·M GribskovD Eisenberg
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Feb 4, 1994·Journal of Molecular Biology·A KroghD Haussler
Feb 1, 1994·Proceedings of the National Academy of Sciences of the United States of America·P BaldiM A McClure
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 12, 1998·Journal of Molecular Biology·C Bystroff, D Baker
Jan 27, 1999·Bioinformatics·S R Eddy
Feb 3, 1999·Bioinformatics·K KarplusR Hughey
Jul 13, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T JaakkolaD Haussler
Aug 5, 2000·Journal of Molecular Biology·C BystroffD Baker
Feb 6, 2002·Journal of Molecular Biology·Golan Yona, Michael Levitt
Aug 10, 2002·Bioinformatics·Koji TsudaKiyoshi Asai
Jul 12, 2003·Bioinformatics·Asa Ben-Hur, Douglas Brutlag
Nov 25, 2003·Bioinformatics·Yuna HouChristopher Bystroff
Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Li Liao, William Stafford Noble
Mar 3, 2004·Bioinformatics·Christina S LeslieWilliam Stafford Noble
Mar 1, 1996·Computers & Chemistry·M Gribskov, N L Robinson

❮ Previous
Next ❯

Citations

Sep 29, 2005·Bioinformatics·Huzefa Rangwala, George Karypis
Dec 15, 2005·Bioinformatics·Yao-Ming Huang, Christopher Bystroff
Jan 25, 2007·Journal of Bioinformatics and Computational Biology·Gek-Huey ChuaMasaru Tomita
Mar 23, 2010·BMC Bioinformatics·Bobbie-Jo M Webb-RobertsonChristopher S Oehmen
Oct 18, 2006·BMC Bioinformatics·Huzefa Rangwala, George Karypis
Jan 27, 2007·BMC Bioinformatics·Tony HåndstadPål Saetrom
Feb 1, 2008·BMC Bioinformatics·John K Vries, Xiong Liu
Apr 10, 2007·Computational Biology and Chemistry·Anuj R ShahBobbie-Jo M Webb-Robertson
May 23, 2006·Current Opinion in Structural Biology·Roland L Dunbrack
Nov 18, 2005·Computational Biology and Chemistry·Bobbie-Jo Webb-RobertsonMelissa Matzke
May 10, 2007·Bioinformatics·Sepp HochreiterKlaus Obermayer

❮ 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

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
T JaakkolaD Haussler
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Li Liao, William S Noble
Journal of Bioinformatics and Computational Biology
Rui KuangChristina Leslie
© 2021 Meta ULC. All rights reserved