AMS 4.0: consensus prediction of post-translational modifications in protein sequences.

Amino Acids
Dariusz PlewczynskiIndrajit Saha

Abstract

We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho.ELM databases for training. The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted from AAindex database. For each type of the numerical representation, the method builds the ensemble of Multi-Layer Perceptron (MLP) pattern classifiers, each optimising different objectives during the training (for example the recall, precision or area under the ROC curve (AUC)). The consensus is built using brainstorming technology, which combines multi-objective instances of machine learning algorithm, and the data fusion of different training objects representations, in order to boost the overall prediction accuracy of conserved short sequence motifs. The performance of AMS 4.0 is compared with the accuracy of previous versions, which were constructed using single machine learning metho...Continue Reading

References

Dec 10, 1998·Nucleic Acids Research·A Bairoch, R Apweiler
Dec 10, 1998·Nucleic Acids Research·S KawashimaM Kanehisa
Dec 11, 1999·Nucleic Acids Research·S Kawashima, M Kanehisa
Dec 22, 1999·Journal of Molecular Biology·N BlomS Brunak
Jun 7, 2002·Bioinformatics·Flavio MonigattiEva Jung
Sep 17, 2002·Briefings in Bioinformatics·Christian J A SigristPhilipp Bucher
Jul 3, 2004·Bioinformatics·Jong Hun KimInsong Koh
Aug 7, 2004·Bioinformatics·Matthias Koenig, Niels Grabe
Feb 25, 2005·Bioinformatics·Dariusz PlewczynskiLeszek Rychlewski
Jun 28, 2005·Nucleic Acids Research·Yu XueXuebiao Yao
Oct 27, 2007·Nucleic Acids Research·Francesca DiellaToby J Gibson
Nov 14, 2007·Nucleic Acids Research·Shuichi KawashimaMinoru Kanehisa
Aug 20, 2009·Protein and Peptide Letters·Songling LiYixue Li
Jan 21, 2010·Journal of Theoretical Biology·Yan XuNai-Yang Deng
Apr 29, 2010·BMC Bioinformatics·Subhadip Basu, Dariusz Plewczynski
May 28, 2010·Bioinformatics·Florian GnadMatthias Mann
Oct 14, 2011·Amino Acids·Indrajit SahaDariusz Plewczynski

❮ Previous
Next ❯

Citations

Dec 12, 2012·Immunogenetics·Indrajit SahaDariusz Plewczynski
Jun 4, 2013·Journal of Molecular Modeling·Brijesh K SriwastavaDariusz Plewczynski
May 10, 2013·PLoS Computational Biology·Janusz M Bujnicki, Jerzy Tiuryn
May 30, 2014·International Journal of Nanomedicine·Sutapa Datta, Subhasis Mukhopadhyay
Mar 13, 2016·Journal of Molecular Modeling·Piyali ChatterjeeDariusz Plewczynski
Dec 20, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Brijesh K SriwastavaUjjwal Maulik
Sep 29, 2015·Briefings in Bioinformatics·Ian WalshSilvio C E Tosatto
Sep 5, 2013·Free Radical Biology & Medicine·André M N SilvaPedro Domingues
Apr 18, 2015·PloS One·Sutapa Datta, Subhasis Mukhopadhyay
Oct 31, 2017·Biomedit︠s︡inskai︠a︡ khimii︠a︡·D A KarasevA A Lagunin
Oct 3, 2017·Briefings in Functional Genomics·Pritha DuttaMahantapas Kundu
Sep 11, 2017·Engineering in Life Sciences·Anupam BanerjeeGeorges Srzednicki
Jun 4, 2020·Omics : a Journal of Integrative Biology·Sayali Chandrashekhar DeolankarThottethodi Subrahmanya Keshava Prasad
Oct 28, 2018·The Protein Journal·Benjamin Yii Chung LauUmi Salamah Ramli

❮ Previous
Next ❯

Methods Mentioned

BETA
acetylation
in silico methods

Software Mentioned

AutoMotifServer
AutoMotif Server (
KinasePhos
Scansite
. ELM
Prot
NetPhosK
PPSP
AutoMotif Service ( AMS )
AMS

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.