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Improving the consistency of domain annotation within the Conserved Domain Database
2015
Database: The Journal of Biological Databases and Curation
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Improving the consistency of domain annotation within the conserved domain database (CDD). ...
Improving domain annotation consistency will in turn reduce the fraction of NR sequences with incomplete DAs. ...
Acknowledgements We thank the Conserved Domain Curators past and present for compiling the domain annotations analyzed in this work, Farideh ...
doi:10.1093/database/bav012
pmid:25767294
pmcid:PMC4356950
fatcat:uyjohnfrnjfrzjyj55me6gs5pa
Recent improvements to the SMART domain-based sequence annotation resource
2002
Nucleic Acids Research
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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 ...
Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. ...
(17) , which contributes to the annotation of SWISS-PROT sequences (5) , and of the Conserved Domain Database (CDD) (http://web.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) which contributes to the annotation ...
doi:10.1093/nar/30.1.242
pmid:11752305
pmcid:PMC99073
fatcat:2v2pjzuwovfttkjqxfapqozday
Digging with Experimental Pick and Computational Shovel: a New Addition to the Histidine Kinase Superfamily
2003
Journal of Bacteriology
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Changing the program to reverse-position-specific BLAST (1), a domain search tool implemented in the conserved domain database (13), does not improve the situation: no conserved SMART or Pfam domains can ...
HISTIDINE KINASES: EASY TARGETS IN MICROBIAL GENOME ANNOTATION Histidine kinases are easy targets for genome annotators because of the significant sequence conservation within the dimerization and ATP-binding ...
They can carry out online annotation of proteins they study, link them to the appropriate peer-reviewed publications, and communicate their suggestions on database improvements directly to the database ...
doi:10.1128/jb.186.2.267-269.2004
pmid:14702293
pmcid:PMC305774
fatcat:f4rowe5vufcffenghgpbqdqvji
Text Mining Improves Prediction of Protein Functional Sites
2012
PLoS ONE
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The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. ...
The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. ...
We would like to thank the software engineering team in the Center for Computational Pharmacology at the University of Colorado School of Medicine: Christophe Roeder for his assistance with infrastructure ...
doi:10.1371/journal.pone.0032171
pmid:22393388
pmcid:PMC3290545
fatcat:4564uparzzb6ldzy2wxjpap2w4
Prot2HG: a database of protein domains mapped to the human genome
2020
Database: The Journal of Biological Databases and Curation
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Database URL: www.prot2hg.com. ...
The location of each exon within the domain interval was stored. ...
Many of the variants were annotated onto multiple domains (43 variants onto 93 domains).
Discussion Genomics has enormously improved the diagnosis of human diseases. ...
doi:10.1093/database/baz161
pmid:32293014
pmcid:PMC7157182
fatcat:fma7anr2dzafnjnjjme2im3wee
Protein domain analysis in the era of complete genomes
2001
FEBS Letters
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Here we address some of the issues involved in better coverage of sequence-based domain annotation, and the integration of these results within the wider context of genomes, structures and function. ß ...
Domains present one of the most useful levels at which to understand protein function, and domain family-based analysis has had a profound impact on the study of individual proteins. ...
Alex Bateman (The Wellcome Trust Sanger Institute) and Chris Ponting (The MRC Functional Genetics Unit, Oxford) for helpful discussions. ...
doi:10.1016/s0014-5793(01)03289-6
pmid:11911892
fatcat:ornwie7ly5ehrm4ltyh7tqiwiq
MMDB: Entrez's 3D-structure database
2003
Nucleic Acids Research
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Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative ...
The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. ...
ACKNOWLEDGEMENTS We thank the NIH Intramural Research Program for support. Questions should be addressed to: info@ncbi.nlm.nih.gov. ...
doi:10.1093/nar/gkg086
pmid:12520055
pmcid:PMC165533
fatcat:6olyiaitk5bi3cgjqufknjd234
MMDB: Entrez's 3D-structure database
2002
Nucleic Acids Research
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Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative ...
The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. ...
ACKNOWLEDGEMENTS We thank the NIH Intramural Research Program for support. Questions should be addressed to: info@ncbi.nlm.nih.gov. ...
doi:10.1093/nar/30.1.249
pmid:11752307
pmcid:PMC99072
fatcat:7h543blngjf6dcned5wqb6uou4
Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life
2012
PLoS Computational Biology
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To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. ...
machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. ...
Tylianakis for valuable comments on the manuscript.
Author Contributions ...
doi:10.1371/journal.pcbi.1002752
pmid:23133357
pmcid:PMC3486863
fatcat:vcxky4j3nzfsnl3ymu7n4xudoq
MiST: a microbial signal transduction database
2007
Nucleic Acids Research
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Because of their extreme sequence variability and extensive domain shuffling, signal transduction proteins are difficult to identify, and their current annotation in most leading databases is often incomplete ...
Newly available, complete genomes are loaded into the database each month. MiST is the only comprehensive and up-to-date electronic catalog of the signaling machinery in microbial genomes. ...
We are grateful to Jan Lukens and 'Friends of the Zhulin lab' for their contribution toward our Linux cluster. ...
doi:10.1093/nar/gkl932
pmid:17135192
pmcid:PMC1747179
fatcat:jhnd255bfjagpafo2irlpzauri
CATH: expanding the horizons of structure-based functional annotations for genome sequences
2018
Nucleic Acids Research
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This article provides an update of the latest data and developments within the CATH protein structure classification database (http://www.cathdb.info). ...
sequence domains, functional annotations and functional clustering (known as Functional Families or FunFams). ...
This enables users to view the domain within the context of the PDB chain ('View Domain in Chain') or in the context of the full PDB ('View Domain in PDB'). ...
doi:10.1093/nar/gky1097
pmid:30398663
fatcat:e3ikbx4aajhbfkwaixxl47qjsu
Comparison of RefSeq protein-coding regions in human and vertebrate genomes
2013
BMC Genomics
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Additionally, 80% of the proteins analyzed pass a suite of tests to detect proteins that lack splicing conservation and have unusual sequence or domain annotation. ...
The process flow described provides specific information on the scope and degree of conservation for the analyzed protein sequences and annotations and will be used to enrich the quality of RefSeq records ...
Acknowledgements This research was supported by the Intramural Research Program of the NIH, National Library of Medicine. ...
doi:10.1186/1471-2164-14-654
pmid:24063302
pmcid:PMC3882889
fatcat:4dtx2aqljjctle2rzc55bayx6m
ELM--the database of eukaryotic linear motifs
2011
Nucleic Acids Research
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Schema of the ELM resource and data life cycle. Annotated ELM classes, and instances thereof, can be searched by database query. ...
The current update of the ELM database comprises 1800 annotated motif instances representing 170 distinct functional classes, including approximately 500 novel instances and 24 novel classes. ...
ACKNOWLEDGEMENTS The authors would like to thank the users of the ELM resource as well as all colleagues, contributors and annotators of the ELM resource. ...
doi:10.1093/nar/gkr1064
pmid:22110040
pmcid:PMC3245074
fatcat:x5kvgzrrnrhczcdxvtm6zoetiq
InterPro in 2017—beyond protein family and domain annotations
2016
Nucleic Acids Research
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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 locations and boundaries (footprints) of known conserved domains, including location of conserved/functional sites. ...
doi:10.1093/nar/gkw1107
pmid:27899635
pmcid:PMC5210578
fatcat:wa7z5pgpuffnrh5bf5ycimw7kq
The MiST2 database: a comprehensive genomics resource on microbial signal transduction
2009
Nucleic Acids Research
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Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification ...
The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. ...
We are especially grateful to Jan Lukens and ''Friends of the Zhulin lab'' for financially supporting the purchase of our Linux cluster. ...
doi:10.1093/nar/gkp940
pmid:19900966
pmcid:PMC2808908
fatcat:qot3dwpmcfamxk7hm2x4wu37jm
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