Improving protein secondary structure prediction using a simple k-mer model.

Bioinformatics
Martin MaderaJulian Gough

Abstract

Some first order methods for protein sequence analysis inherently treat each position as independent. We develop a general framework for introducing longer range interactions. We then demonstrate the power of our approach by applying it to secondary structure prediction; under the independence assumption, sequences produced by existing methods can produce features that are not protein like, an extreme example being a helix of length 1. Our goal was to make the predictions from state of the art methods more realistic, without loss of performance by other measures. Our framework for longer range interactions is described as a k-mer order model. We succeeded in applying our model to the specific problem of secondary structure prediction, to be used as an additional layer on top of existing methods. We achieved our goal of making the predictions more realistic and protein like, and remarkably this also improved the overall performance. We improve the Segment OVerlap (SOV) score by 1.8%, but more importantly we radically improve the probability of the real sequence given a prediction from an average of 0.271 per residue to 0.385. Crucially, this improvement is obtained using no additional information. http://supfam.cs.bris.ac.uk/kmer

References

Jul 20, 1993·Journal of Molecular Biology·B Rost, C Sander
Jun 1, 1996·Methods : a Companion to Methods in Enzymology·M Malmqvist
Feb 3, 1999·Bioinformatics·J A CuffG J Barton
Jul 13, 2000·Protein Science : a Publication of the Protein Society·M Ouali, R D King
Aug 5, 2000·Journal of Molecular Biology·C BystroffD Baker
Apr 6, 2001·Physical Review Letters·F Wang, D P Landau
Oct 5, 2002·Nucleic Acids Research·Martin Madera, Julian Gough
Jan 28, 2003·Journal of Molecular Biology·Ruslan Sadreyev, Nick Grishin
Jun 26, 2003·Nucleic Acids Research·Ingrid Y Y KohBurkhard Rost
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Nov 9, 2004·Bioinformatics·Johannes Söding
Dec 9, 2004·Bioinformatics·Gianluca Pollastri, Aoife McLysaght
Oct 6, 2005·Bioinformatics·Kengo Sato, Yasubumi Sakakibara
Jul 29, 2006·Bioinformatics·Chuong B DoSerafim Batzoglou
Sep 2, 2008·Bioinformatics·Sol KatzmanKevin Karplus
Jun 2, 2009·Nucleic Acids Research·Kevin Karplus
Dec 7, 2005·Physical Chemistry Chemical Physics : PCCP·David J Earl, Michael W Deem

❮ Previous
Next ❯

Citations

May 9, 2012·Journal of Molecular Modeling·S SaraswathiA Kloczkowski
Jun 30, 2012·Nature Methods·Kevin W EliceiriAnne E Carpenter
Jan 13, 2011·Bioinformatics·Yi ZhangLe Kang
Nov 13, 2010·Nucleic Acids Research·Robbie P JoostenGert Vriend
Feb 18, 2011·Journal of Bioinformatics and Computational Biology·Kanaka Durga KedarisettiLukasz Kurgan
Feb 22, 2011·Journal of Theoretical Biology·Alexandre G de Brevern, Agnel Praveen Joseph
Jan 10, 2013·Journal of Biomolecular Structure & Dynamics·Jing YanLukasz Kurgan
Oct 11, 2016·PloS One·Shunian XiangZhirong Sun
Nov 20, 2018·F1000Research·Linhua WangGaurav Pandey

❮ Previous
Next ❯

Software Mentioned

HMMSTR
CASP
EVA
PREDICT
PISCES
STR2
- 2ND

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.