ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes

PloS One
Linh TranBurkhard Rost

Abstract

Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods. We extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae. Those data were the base to develop a PPI prediction method for each model organism. The method used evolutionary information through a profile-kernel Support Vector Machine (SVM). With the resulting eight models, we predicted all possible protein pairs in each organism and made the top predictions available through a web application. Almost all of the PPIs made available were predicted between proteins that have not been observed in any inter...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Apr 9, 1999·Protein Engineering·B Rost
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Feb 25, 2000·Biological Psychiatry·R M BermanJ H Krystal
Feb 17, 2001·Current Opinion in Structural Biology·J H LaityP E Wright
Aug 24, 2001·Journal of Molecular Biology·E Sprinzak, H Margalit
Mar 26, 2002·FEBS Letters·Andreas ZanzoniGianni Cesareni
Aug 10, 2002·Bioinformatics·Trey IdekerAndrew F Siegel
Aug 21, 2004·Bioinformatics·Shawn MartinJean-Loup Faulon
Aug 19, 2005·Journal of Bioinformatics and Computational Biology·Rui KuangChristina Leslie
Oct 7, 2005·Genome Biology·Robert RileyDavid Eisenberg
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Dec 6, 2006·Nucleic Acids Research·S KerrienH Hermjakob
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Juwen ShenHualiang Jiang
May 13, 2008·Drug Discovery Today·Yin LiuHongyu Zhao
Jan 21, 2009·Bioinformatics·Xue-wen Chen, Jong Cheol Jeong
Nov 19, 2009·Nucleic Acids Research·Pawel SmialowskiAndreas Ruepp
Aug 31, 2010·Bioinformatics·Jiantao YuDavid R Westhead
Nov 30, 2010·Nucleic Acids Research·Anja JankowskyEckhard Jankowsky
Feb 22, 2012·PloS One·Martin H SchaeferMiguel A Andrade-Navarro
Feb 23, 2012·Scientific Reports·Sylvain PitreAshkan Golshani
Dec 12, 2012·Nature Methods·Yungki Park, Edward M Marcotte
Jul 31, 2013·Current Opinion in Structural Biology·Roberto MoscaPatrick Aloy
Aug 1, 2013·Nature Methods·Alberto CalderoneGianni Cesareni
Jul 30, 2014·Bioinformatics·Erik L L SonnhammerUNKNOWN Quest for Orthologs consortium
Nov 25, 2014·Cell·Thomas RollandMarc Vidal
Jan 15, 2015·Bioinformatics·Tobias Hamp, Burkhard Rost
Feb 7, 2015·Bioinformatics·Tobias Hamp, Burkhard Rost
Jun 9, 2015·IEEE Transactions on Cybernetics·Shuai LiZhong-Qiu Zhao
Nov 20, 2015·Nucleic Acids Research·Radek SzklarczykMartijn A Huynen

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
pull down
enzyme linked immunosorbent assay
protein folding

Software Mentioned

MINT
Mentha
PSI
ProfPPIdb
SigProd
DIP
BLAST
PredictProtein
STRING
IntAct

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.

© 2022 Meta ULC. All rights reserved