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Pattern Recognition for Subfamily Level Classification of GPCRs Using Motif Distillation and Distinguishing Power Evaluation
[chapter]
2012
Lecture Notes in Computer Science
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Our results indicate that in Family A Peptide subfamily, 91% of all proteins listed in GPCRdb can be covered by using only 691 different motifs, which can be employed later as an invaluable source for ...
G protein coupled receptors (GPCRs) are one of the most prominent and abundant family of membrane proteins in the human genome. ...
sites and family specific motifs using only the protein sequence information. ...
doi:10.1007/978-3-642-34123-6_24
fatcat:4rxlo7ethjg5lkyc4wvpdbffmy
PRED-GPCR: GPCR recognition and family classification server
2004
Nucleic Acids Research
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PRED-GPCR is a free Internet service for GPCR recognition and classification at the family level. ...
The vast cell-surface receptor family of G-protein coupled receptors (GPCRs) is the focus of both academic and pharmaceutical research due to their key role in cell physiology along with their amenability ...
However, the task of automatic classification of novel GPCRs into one of the functional families, as defined by ligand specificity, is not always straightforward. ...
doi:10.1093/nar/gkh431
pmid:15215415
pmcid:PMC441569
fatcat:gc5ijklqdjatromhl2bde6l42a
Prediction and Classification for GPCR Sequences Based on Ligand Specific Features
[chapter]
2006
Lecture Notes in Computer Science
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The method also tells us which motifs are significant for class determination which has important design implications. ...
Therefore, classification methods for automated characterization of orphan GPCRs are imperative. ...
Prediction and Classification for GPCR Sequences ...
doi:10.1007/11902140_20
fatcat:w4xvt7ypbveflbxtb5bk6l6m3u
A brief review on the evolution of GPCR: conservation and diversification
2012
Open Journal of Genetics
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Here, we briefly discuss evolutionary dynamic mechanism of GPCR from the perspective of classification, diversification and conservation. ...
Many investigations focus on fine structure shaping and GPCR classification. ...
Republic of China for supporting this work. ...
doi:10.4236/ojgen.2012.24b003
fatcat:nt76em3ps5bwvaxqm4dtd2jxkq
Proteomic applications of automated GPCR classification
2007
Proteomics
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Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free ...
Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. ...
Protein family databases are developed using multiple sequence alignment of the family of interest and identifying the most conserved regions to be the basis of family motifs. ...
doi:10.1002/pmic.200700093
pmid:17639603
fatcat:5yciwuejezb73erfw2qs5g3cka
Construction of a sequence motif characteristic of aminergic G protein-coupled receptors
2003
Protein Science
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A number of orphan GPCRs assigned to the aminergic class by this motif were later discovered to be a novel subfamily of trace amine GPCRs, as well as the successful classification of the histamine H4 receptor ...
This minimally defined motif is an appropriate computational tool for identifying additional, potentially novel aminergic GPCRs from a set of experimentally uncharacterized "orphan" GPCRs, complementing ...
The key differences between the excellent and comprehensive work by Attwood and coworkers (2002) on motif-based GPCR classification and the present one relate to specificity, scope, and throughput. ...
doi:10.1110/ps.0305603
pmid:12824482
pmcid:PMC2323918
fatcat:5tpdfnhudfdh7nv7pnwo5cxvfa
Present Perspectives on the Automated Classification of the G-Protein Coupled Receptors (GPCRs) at the Protein Sequence Level
2011
Current Topics in Medicinal Chemistry
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We review here the available methodologies for the classification of GPCRs. ...
Part of this work focuses on how we have tried to build the intrinsically hierarchical nature of sequence relations, implicit within the family, into an adaptive approach to classification. ...
A motif-based approach was used whereby InterPro estimated the total number of Rhodopsin-like GPCRs to be 569 [71] . ...
doi:10.2174/156802611796391221
pmid:21470173
fatcat:bq5tvhcbm5d4dkudb4y5andlne
Bioinformatics approaches for the classification of G-protein-coupled receptors
2003
Current opinion in pharmacology (Print)
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However, the use of such programs in identifying families and predicting ligands for orphan GPCRs is limited. ...
the overlapping coupling specificity of receptors in this family. ...
doi:10.1016/s1471-4892(03)00005-5
pmid:12681231
fatcat:o63h6i3mnna2fhx2mmx7b7a4uq
SVM Model for Identification of human GPCRs
[article]
2010
arXiv
pre-print
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Classification is based on specific information derived from the n-terminal and extracellular loops of the sequences, some physicochemical properties and amino acid composition of corresponding gpcr sequences ...
GPCRs are usually classified into several functionally distinct families that play a key role in cellular signalling and regulation of basic physiological processes. ...
GPCRs can be grouped into six distinct classes A,B,C,D,E and frizzled/Smoothened family as defined by GPCRDB classification on the base of shared sequence motifs [15] . ...
arXiv:1002.3983v1
fatcat:4iqv4r73vbcx3hrwev45qiis34
Deriving structural and functional insights from a ligand-based hierarchical classification of G protein-coupled receptors
2002
Protein Engineering Design & Selection
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G protein-coupled receptors (GPCRs) constitute the largest known family of cell-surface receptors. ...
This resource forms part of the PRINTS database, which now houses~250 GPCR-specific fingerprints (http:// www.bioinf.man.ac.uk/dbbrowser/gpcrPRINTS/). ...
Acknowledgements PRINTS is built and maintained at the University of Manchester with support from the Royal Society (T.K.A. is a Royal Society University Research Fellow). ...
doi:10.1093/protein/15.1.7
pmid:11842232
fatcat:5xckkj72ofhsrlgdcvrqtm6yvy
The extracellular N-terminal domain suffices to discriminate class C G Protein-Coupled Receptor subtypes from n-grams of their sequences
2015
2015 International Joint Conference on Neural Networks (IJCNN)
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of n-grams whose length of up to five amino acids opens up an avenue for class C GPCR signature motif discovery. ...
We report experiments that show that the extracellular N-terminal domain of the receptor suffices to retain the classification accuracy of the complete sequence and that it does so using a reduced selection ...
classification methods for the classification of GPCRs [19] . ...
doi:10.1109/ijcnn.2015.7280613
dblp:conf/ijcnn/KonigAVG15
fatcat:qyadecrkqbhjdlx3deb5ngdo3i
GPCR-SAS: A web application for statistical analyses on G protein-coupled receptors sequences
2018
PLoS ONE
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G protein-coupled receptors (GPCRs) are one of the largest protein families in mammals. ...
acids in two positions (or two sequence motifs in two ranges of positions), and (iv) snake-plot representation for a specific receptor or for the consensus sequence of a group of selected receptors. ...
The gray arrow indicates that it is possible to get the list of receptors that contain a certain residue or motif. https://doi.org/10.1371/journal.pone.0199843.g004 ...
doi:10.1371/journal.pone.0199843
pmid:30044824
pmcid:PMC6059404
fatcat:sphkqjd3uzdotdjiyasciggry4
Specific Peptides Predict Protein Classification
[article]
2022
bioRxiv
pre-print
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We also apply this method to two other protein families, GPCR and ZF, find their corresponding SPs, and provide the code for searching any protein sequence for its classification under any such family. ...
The methodology of Specific Peptides (SP) has been introduced within the context of enzymes. ...
This procedure leads to the reduction of the set of motifs to 286,755 specific peptides which we label as ESPs. ...
doi:10.1101/2022.02.04.479085
fatcat:vmgwewbsjngwllriiv42wwppvq
Prediction of G Protein-Coupled Receptors with SVM-Prot Features and Random Forest
2016
Scientifica
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MEME suite was used to detect the most significant 10 conserved motifs of human GPCRs. In the testing datasets, the average accuracy was 91.61%, and the average AUC was 0.9282. ...
MEME discovery analysis showed that many motifs aggregated in the seven hydrophobic helices transmembrane regions adapt to the characteristic of GPCRs. ...
Conserved Motif Analyses of Human GPCR Proteins. Online MEME Suite 4.11.0 (http://meme-suite.org/) was used to analyze conserved motif analyses. ...
doi:10.1155/2016/8309253
pmid:27529053
pmcid:PMC4978840
fatcat:q5cdcorkbveklivog7iaoipfu4
Selecting different protein representations and classification algorithms in hierarchical protein function prediction
2011
Intelligent Data Analysis
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There are several ways of extracting features from a protein, and the choice of the feature representation might be as important as the choice of the classification algorithm. ...
There are two major problems in the task of computational protein function prediction, which are the choice of the protein representation and the choice of the classification algorithm. ...
Considering the results specifically for GPCRs, the LD provides very good results (except for the GPCR-Interpro, in which its results are similar to the results of the motif representation) considering ...
doi:10.3233/ida-2011-0505
fatcat:e7uy3xr55nhsrbks4i7jm6zfpu
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