Filters








50,852 Hits in 3.8 sec

Improving the consistency of domain annotation within the Conserved Domain Database

Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Jane He, Gabriele H. Marchler, Zhouxi Wang, Aron Marchler-Bauer
2015 Database: The Journal of Biological Databases and Curation  
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

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  ...  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

I. B. Zhulin
2003 Journal of Bacteriology  
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

Karin M. Verspoor, Judith D. Cohn, Komandur E. Ravikumar, Michael E. Wall, Neil R. Smalheiser
2012 PLoS ONE  
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  
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

Richard R. Copley, Tobias Doerks, Ivica Letunic, Peer Bork
2001 FEBS Letters  
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

J. Chen
2003 Nucleic Acids Research  
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

Y. Wang
2002 Nucleic Acids Research  
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

Marc P. Hoeppner, Paul P. Gardner, Anthony M. Poole, Claus O. Wilke
2012 PLoS Computational Biology  
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

L. E. Ulrich, I. B. Zhulin
2007 Nucleic Acids Research  
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

Ian Sillitoe, Natalie Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, Paul Ashford, Adeyelu Tolulope, Harry M Scholes, Ilya Senatorov, Andra Bujan, Fatima Ceballos Rodriguez-Conde, Benjamin Dowling (+2 others)
2018 Nucleic Acids Research  
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

Jessica H Fong, Terence D Murphy, Kim D Pruitt
2013 BMC Genomics  
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

H. Dinkel, S. Michael, R. J. Weatheritt, N. E. Davey, K. Van Roey, B. Altenberg, G. Toedt, B. Uyar, M. Seiler, A. Budd, L. Jodicke, M. A. Dammert (+17 others)
2011 Nucleic Acids Research  
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

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 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

Luke E. Ulrich, Igor B. Zhulin
2009 Nucleic Acids Research  
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
« Previous Showing results 1 — 15 out of 50,852 results