PPAI: a web server for predicting protein-aptamer interactions

BMC Bioinformatics
Jianwei LiJunhua Gu

Abstract

The interactions between proteins and aptamers are prevalent in organisms and play an important role in various life activities. Thanks to the rapid accumulation of protein-aptamer interaction data, it is necessary and feasible to construct an accurate and effective computational model to predict aptamers binding to certain interested proteins and protein-aptamer interactions, which is beneficial for understanding mechanisms of protein-aptamer interactions and improving aptamer-based therapies. In this study, a novel web server named PPAI is developed to predict aptamers and protein-aptamer interactions with key sequence features of proteins/aptamers and a machine learning framework integrated adaboost and random forest. A new method for extracting several key sequence features of both proteins and aptamers is presented, where the features for proteins are extracted from amino acid composition, pseudo-amino acid composition, grouped amino acid composition, C/T/D composition and sequence-order-coupling number, while the features for aptamers are extracted from nucleotide composition, pseudo-nucleotide composition (PseKNC) and normalized Moreau-Broto autocorrelation coefficient. On the basis of these feature sets and balanced the...Continue Reading

References

Nov 1, 1971·Proceedings of the National Academy of Sciences of the United States of America·C Delisi, D M Crothers
Sep 12, 1995·Proceedings of the National Academy of Sciences of the United States of America·I DubchakS H Kim
Oct 24, 2000·Journal of Protein Chemistry·Z P Feng, C T Zhang
Mar 25, 2004·The Journal of Biological Chemistry·Manoj Bhasin, Gajendra P S Raghava
Jul 23, 2011·PLoS Computational Biology·William S SandersKenneth O Willeford
Mar 22, 2012·Database : the Journal of Biological Databases and Curation·Jose Cruz-ToledoMichel Dumontier
Mar 23, 2013·Journal of Translational Medicine·Ankur GautamGajendra P S Raghava
Mar 26, 2013·BMC Bioinformatics·Rok Blagus, Lara Lusa
Sep 21, 2013·Protein Engineering, Design & Selection : PEDS·Hua-Lin XieXi-Du Nie
Dec 3, 2014·Medical Decision Making : an International Journal of the Society for Medical Decision Making·Azra RamezankhaniDavood Khalili
May 1, 2015·BMC Bioinformatics·Ivan LimongelliRiccardo Bellazzi
Oct 28, 2016·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Kei X TanSie Yon Lau
Jan 8, 2017·Annual Review of Pharmacology and Toxicology·Shahid M NimjeeBruce A Sullenger
Aug 2, 2017·Medicinal Research Reviews·Maryam Sadat NabaviniaKhalil Abnous
Sep 14, 2017·Scientific Reports·Raziur RahmanRanadip Pal
Oct 1, 2017·Biochimie·Vittorio de Franciscis

❮ Previous
Next ❯

Methods Mentioned

BETA
interaction prediction
feature extraction
interaction

Software Mentioned

pROC
Predict Aptamer
EasyUI
iFeature
NMBAC
sklearn
pseKNC
Adaboost
RNAfold
MySQL

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.