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UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

Tunca Doğan, Alistair MacDougall, Rabie Saidi, Diego Poggioli, Alex Bateman, Claire O'Donovan, Maria J. Martin
2016 Bioinformatics  
Results: We propose a method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities  ...  and propagating functional annotation.  ...  Here, we present the UniProt Domain Architecture Alignment and Classification (DAAC) procedure for the automatic annotation of uncharacterized proteins in UniProtKB based upon domain architectural similarity  ... 
doi:10.1093/bioinformatics/btw114 pmid:27153729 pmcid:PMC4965628 fatcat:dwuwcqp4wvclvhyr4fqoqx2gea

MDPFP-FCNN: Multidomain Protein Function Prediction Using Fuzzy Convolutional Neural Network

2021 International Journal of Intelligent Engineering and Systems  
In this research, we used a model for predicting multi-domain protein function using a Fuzzy Convolutional Neural Network.  ...  In this research, we used a novel hybrid CNN and Fuzzy for sequence labelling, specifically to predict the function of the protein.  ...  Doğan, et al. ( 2016 ) used a novel approach (UniProt-DAAC) in the field of automatic functional annotation of protein sequences with the alignment and classification of domain architectures (DAs). (  ... 
doi:10.22266/ijies2021.1231.57 fatcat:bpexbfonj5c25kxlsmnjmbnb6q

Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases

Tunca Doğan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Martin, Rengul Cetin-Atalay, Feixiong Cheng
2021 PLoS Computational Biology  
Here, we propose a new method "DRUIDom" (DRUg Interacting Domain prediction) to identify bio-interactions between drug candidate compounds and targets by utilizing the domain modularity of proteins, to  ...  As such, other proteins containing the same mapped domain or domain pair become new candidate targets for the corresponding compounds.  ...  For this, all domain pair combinations were identified for each target protein in our source dataset, using the domain architecture information of the proteins extracted using the UniProt-DAAC method,  ... 
doi:10.1371/journal.pcbi.1009171 pmid:34843456 pmcid:PMC8659301 fatcat:5yvxwtolfrejhl2v5r4nvzif6u