Development of a novel bioinformatics tool for in silico validation of protein interactions.

Journal of Biomedicine & Biotechnology
Nicola BarbariniRiccardo Bellazzi

Abstract

Protein interactions are crucial in most biological processes. Several in silico methods have been recently developed to predict them. This paper describes a bioinformatics method that combines sequence similarity and structural information to support experimental studies on protein interactions. Given a target protein, the approach selects the most likely interactors among the candidates revealed by experimental techniques, but not yet in vivo validated. The sequence and the structural information of the in vivo confirmed proteins and complexes are exploited to evaluate the candidate interactors. Finally, a score is calculated to suggest the most likely interactors of the target protein. As an example, we searched for GRB2 interactors. We ranked a set of 46 candidate interactors by the presented method. These candidates were then reduced to 21, through a score threshold chosen by means of a cross-validation strategy. Among them, the isoform 1 of MAPK14 was in silico confirmed as a GRB2 interactor. Finally, given a set of already confirmed interactors of GRB2, the accuracy and the precision of the approach were 75% and 86%, respectively. In conclusion, the proposed method can be conveniently exploited to select the proteins to ...Continue Reading

References

Jul 5, 1990·Journal of Molecular Biology·D G KnellerR Langridge
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
May 20, 1994·Journal of Molecular Biology·I K McDonald, J M Thornton
Feb 17, 1998·Protein Engineering·D XuR Nussinov
Feb 17, 2000·Cellular Signalling·K Ono, J Han
Mar 1, 2000·Trends in Biochemical Sciences·C CombetG Deléage
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Juan Fernández-RecioRuben Abagyan
Mar 5, 2002·European Journal of Biochemistry·Piero FariselliRita Casadio
Jul 20, 2002·Current Opinion in Structural Biology·Alfonso Valencia, Florencio Pazos
Jan 10, 2003·Nucleic Acids Research·Gary D BaderChristopher W V Hogue
Apr 26, 2003·The Journal of Investigative Dermatology·Richard L EckertShervin Dashti
Jun 5, 2003·FEBS Letters·Yanay Ofran, Burkhard Rost
Jul 2, 2003·Current Opinion in Structural Biology·Lukasz Salwinski, David Eisenberg
Dec 19, 2003·Nucleic Acids Research·Lukasz SalwinskiDavid Eisenberg
Dec 19, 2003·Nucleic Acids Research·Suraj PeriAkhilesh Pandey
Dec 23, 2003·Journal of Molecular Biology·Juan Fernández-RecioRuben Abagyan
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Jun 28, 2005·Proteins·Yuval InbarHaim J Wolfson
Jun 28, 2005·Proteins·A D J van DijkA M J J Bonvin
Jun 28, 2005·Proteins·Juan Fernández-RecioMaxim Totrov
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Feb 16, 2006·Journal of Molecular Biology·William A McLaughlinWei Wang
Sep 15, 2006·The Journal of Physical Chemistry. a·Mirosław JabłońskiAndrzej J Sadlej
Dec 21, 2007·Molecular Biotechnology·Lucy SkrabanekAnton J Enright
Apr 26, 2008·Current Opinion in Structural Biology·Yang Zhang
Jul 26, 2008·Proteins·Nelly AndrusierHaim J Wolfson
Aug 12, 2008·Current Protein & Peptide Science·Sjoerd J de Vries, Alexandre M J J Bonvin
Oct 22, 2008·Journal of Molecular Biology·Maricel G KannTeresa M Przytycka
Apr 7, 2009·Briefings in Bioinformatics·Iakes EzkurdiaMichael L Tress
Apr 28, 2009·Current Opinion in Structural Biology·Ruben E ValasPhilip E Bourne
Sep 5, 2009·Proteins·Carles PonsJuan Fernández-Recio
Oct 6, 2009·Biochemical and Biophysical Research Communications·Hung Xuan Ta, Liisa Holm

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
two
affinity purification
in silico methods
nuclear translocation
pull-down
two hybrids

Software Mentioned

NPS
PREDATOR
PINT
ConSurf
NNPREDICT
CINT

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.