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SMART 7: recent updates to the protein domain annotation resource

I. Letunic, T. Doerks, P. Bork
2011 Nucleic Acids Research  
SMART (Simple Modular Architecture Research Tool) is an online resource (http://smart.embl.de/) for the identification and annotation of protein domains and the analysis of protein domain architectures  ...  SMART version 7 contains manually curated models for 1009 protein domains, 200 more than in the previous version.  ...  USER INTERFACE IMPROVEMENTS Version 7 brings various updates to SMART's web interface.  ... 
doi:10.1093/nar/gkr931 pmid:22053084 pmcid:PMC3245027 fatcat:imrz5awrsrecnpspq4ui3gkzu4

SMART 6: recent updates and new developments

I. Letunic, T. Doerks, P. Bork
2009 Nucleic Acids Research  
Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains.  ...  As an initial step towards integrating information on biological pathways into SMART, our domain annotations were extended with data on metabolic pathways and links to several pathways resources.  ...  Domain annotation pages have also been redesigned and updated.  ... 
doi:10.1093/nar/gkn808 pmid:18978020 pmcid:PMC2686533 fatcat:unkoeykctbgb7lfoakzf5crfm4

20 years of the SMART protein domain annotation resource

Ivica Letunic, Peer Bork
2017 Nucleic Acids Research  
SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures.  ...  The underlying protein databases were synchronized with UniProt (2), Ensembl (3) and STRING (4), doubling the total number of annotated domains and other protein features to more than 200 million.  ...  of SMART.  ... 
doi:10.1093/nar/gkx922 pmid:29040681 pmcid:PMC5753352 fatcat:5kb5keptorg57gmddprpubq4ja

SMART: recent updates, new developments and status in 2015

Ivica Letunic, Tobias Doerks, Peer Bork
2014 Nucleic Acids Research  
SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain  ...  In the current version, SMART contains manually curated models for more than 1200 protein domains, with ∼200 new models since our last update article.  ...  UPDATED PROTEIN DATABASES The main protein database in SMART consists of the complete UniProt protein database (7) combined with predicted proteins from all stable Ensembl (8) genomes.  ... 
doi:10.1093/nar/gku949 pmid:25300481 pmcid:PMC4384020 fatcat:yfkluv6fgvepzl6quev6z26cxq

Recent improvements to the SMART domain-based sequence annotation resource

I. Letunic
2002 Nucleic Acids Research  
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular  ...  We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL.  ...  SMART has also been incorporated into other domain and protein family resources that are used for the primary annotation of sequence databases.  ... 
doi:10.1093/nar/30.1.242 pmid:11752305 pmcid:PMC99073 fatcat:2v2pjzuwovfttkjqxfapqozday

SMART, a simple modular architecture research tool: Identification of signaling domains

J. Schultz, F. Milpetz, P. Bork, C. P. Ponting
1998 Proceedings of the National Academy of Sciences of the United States of America  
SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains  ...  Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid  ...  J.S. and P.B were supported by the European Union, Bundesministerium für Bildung und Forschung (Germany), and the Deutsche Forschungsgemeinschaft.  ... 
doi:10.1073/pnas.95.11.5857 pmid:9600884 pmcid:PMC34487 fatcat:fl4mqv46ffe5lirayduumwbqgy

SMART 5: domains in the context of genomes and networks

I. Letunic
2006 Nucleic Acids Research  
The Simple Modular Architecture Research Tool 10 (SMART) is an online resource (http://smart.embl. de/) used for protein domain identification and the analysis of protein domain architectures.  ...  Domain annotation has been updated with a detailed taxonomic breakdown and a prediction of the catalytic activity for 50 SMART domains is now 20 available, based on the presence of essential amino acids  ...  The domain architecture is defined as the linear order of all SMART domains in the protein sequence.20 To derive the point of its invention, all proteins with the same domain architecture are mapped onto  ... 
doi:10.1093/nar/gkj079 pmid:16381859 pmcid:PMC1347442 fatcat:budessywujfidkxtegs7jntvzi

STRING 7--recent developments in the integration and prediction of protein interactions

C. von Mering, L. J. Jensen, M. Kuhn, S. Chaffron, T. Doerks, B. Kruger, B. Snel, P. Bork
2007 Nucleic Acids Research  
Novel features include AJAX-based web-navigation, inclusion of additional resources such as BioGRID, and detailed protein domain annotation. STRING is available at http:// string.embl.de/  ...  The database and online resource STRING generalizes access to protein interaction data, by integrating known and predicted interactions from a variety of sources.  ...  ACKNOWLEDGEMENTS The authors wish to thank Dianna Fisk from the Saccharomyces Genome Database for access to the Gene Summary Paragraphs, and Toby Gibson, Martijn Huynen, Victor Neduva, Rune Linding and  ... 
doi:10.1093/nar/gkl825 pmid:17098935 pmcid:PMC1669762 fatcat:tlao5nbbsvbl7i6wngzibx5j3y

Sensors and Actuators in Smart Cities

Mohammad Hammoudeh, Mounir Arioua
2018 Journal of Sensor and Actuator Networks  
The authors are grateful to the Middle East University, Amman, Jordan for the financial support granted to cover the publication fee of this research article. Author Contributions: Abdelhamied A.  ...  Author Contributions: Alex Adim Obinikpo and Burak Kantarci conceived and pursued the literature survey on deep learning techniques on big sensed data for smart health applications, reviewed the state  ...  As recent research states, proper management and development of smart health is the key to success of the smart city ecosystem [6] .  ... 
doi:10.3390/jsan7010008 fatcat:pt7nkf4oaraijkmsndohahqtnq

Domains, motifs and clusters in the protein universe

Jinfeng Liu, Burkhard Rost
2003 Current Opinion in Chemical Biology  
JL and BR were supported by the grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH).  ...  Last, not least, thanks to all those who deposit their experimental data in public databases, and to those who maintain these databases.  ...  Here, we reviewed some of the recent manual and automatic methods that attempt to classify proteins (URLs in Table 1 ). Expert-curated databases of protein families Motifs and domains.  ... 
doi:10.1016/s1367-5931(02)00003-0 pmid:12547420 fatcat:3etuaqalbnbr5hxzdbajd3cdrq

Genome cartography through domain annotation

C P Ponting, N J Dickens
2001 Genome Biology  
To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as  ...  Although the protein repertoires of distantly related species differ greatly, their domain repertoires do not.  ...  The resources were used to annotate the proteome according to lists of component domains rather than protein or gene names.  ... 
pmid:11521679 fatcat:57ewcgr5obautgpysl3afg45ci

The Pfam protein families database in 2019

Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart, Erik L L Sonnhammer, Layla Hirsh (+4 others)
2018 Nucleic Acids Research  
We recently began to collaborate with the RepeatsDB resource to improve the definition of tandem repeat families within Pfam.  ...  We carried out a significant comparison to the structural classification database, namely the Evolutionary Classification of Protein Domains (ECOD) that led to the creation of 825 new families based on  ...  ACKNOWLEDGEMENTS We would like to thank the various members of the EMBL-European Bioinformatics Institute training team for their assistance in developing the online training materials.  ... 
doi:10.1093/nar/gky995 pmid:30357350 pmcid:PMC6324024 fatcat:q5wtvxfqzzhobpis5p4d2g6wue

Smart Data for Genomic Information Systems: the SILE Method

Ana León Palacio, Óscar Pastor López
2018 Complex Systems Informatics and Modeling Quarterly  
By using conceptual models and the principles of data quality management, adapted to the genomic domain, we propose a systematic approach called the SILE method to move from a Big Data to a Smart Data  ...  levels of quality; but when data are used to solve a concrete problem only, a small part of that "data lake" is really significant; this is what we call the "smart" data perspective.  ...  Acknowledgement The authors would like to thank the members of the PROS Research Centre Genome group for the fruitful discussions regarding the application of CM in the medicine field.  ... 
doi:10.7250/csimq.2018-17.01 fatcat:g6kkf5uqpzh7fctqwd7d7kuqhq

Breeding Climate-Resilient Bananas [chapter]

Allan Brown, Sebastien C. Carpentier, Rony Swennen
2020 Genomic Designing of Climate-Smart Fruit Crops  
Acknowledgements This study has been supported by Grants Nº 19308/PI/14 and Nº 19879/GERM/15 of the Seneca Foundation of the Region of Murcia and the Apricot Breeding project Converse (1987) , Tzanetakis  ...  (TFs) such as WRKY and NAC domain-containing proteins.  ...  Under water stress, they protect the hydrophobic domains of enzymes from exposure to the solvent, help maintaining the high-ordered water molecules surrounding the proteins, and prevent structural changes  ... 
doi:10.1007/978-3-319-97946-5_4 fatcat:cqzcfw6fnfcjtbnsw2bchzkx3q

InterPro in 2017—beyond protein family and domain annotations

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft (+35 others)
2016 Nucleic Acids Research  
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites.  ...  Here, we report recent developments with InterPro and its associated software, in-cluding the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and  ...  The member database updates that contributed to recent InterPro releases are shown in Table 1 .  ... 
doi:10.1093/nar/gkw1107 pmid:27899635 pmcid:PMC5210578 fatcat:wa7z5pgpuffnrh5bf5ycimw7kq
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