Research Topics
| Aron Marchler-BauerSummaryAffiliation: National Institutes of Health Country: USA Publications
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Detail Information
Publications
CDD: conserved domains and protein three-dimensional structureAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 41:D348-52. 2013..To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts...- CDD: specific functional annotation with the Conserved Domain DatabaseAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 37:D205-10. 2009.... - CDD: a conserved domain database for interactive domain family analysisAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 35:D237-40. 2007..More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies... - CDD: a Conserved Domain Database for protein classificationAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 33:D192-6. 2005..Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system... - CD-Search: protein domain annotations on the flyAron Marchler-Bauer
Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 32:W327-31. 2004..CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi... - CDD: a curated Entrez database of conserved domain alignmentsAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 31:383-7. 2003..This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members... - CDD: a database of conserved domain alignments with links to domain three-dimensional structureAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 30:281-3. 2002..CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST... - CDD: a Conserved Domain Database for the functional annotation of proteinsAron Marchler-Bauer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 39:D225-9. 2011..CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml... - Database resources of the National Center for Biotechnology InformationEric W Sayers
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 40:D13-25. 2012..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - MMDB: annotating protein sequences with Entrez's 3D-structure databaseYanli Wang
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 35:D298-300. 2007..The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure)... - IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteinsBenjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
Nucleic Acids Res 40:D834-40. 2012..The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly... - MMDB: Entrez's 3D-structure databaseJie Chen
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 31:474-7. 2003..MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html... - MMDB: Entrez's 3D-structure databaseYanli Wang
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 30:249-52. 2002..MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure... - The NCBI BioSystems databaseLewis Y Geer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D492-6. 2010.... - Database resources of the National Center for Biotechnology InformationEric W Sayers
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 39:D38-51. 2011..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sitesBenjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D518-24. 2010..IBIS is updated regularly and is freely accessible via http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html... - MMDB: 3D structures and macromolecular interactionsThomas Madej
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 40:D461-4. 2012..MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure... 
Comparison of sequence and structure alignments for protein domainsAron Marchler-Bauer
Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
Proteins 48:439-46. 2002..These observations suggest that structure comparison results might be used to improve the overall accuracy of domain alignment collections and the performance of profile search methods based on them...- CORAL: aligning conserved core regions across domain familiesJessica H Fong
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Bioinformatics 25:1862-8. 2009..To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units... - Database resources of the National Center for Biotechnology InformationEric W Sayers
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D5-16. 2010..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - Annotation of functional sites with the Conserved Domain DatabaseMyra K Derbyshire
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
Database (Oxford) 2012:bar058. 2012.... - Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomesViswanadham Sridhara
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD, USA
Database (Oxford) 2011:bar019. 2011..sapiens, M. musculus and D. melanogaster. The method scales automatically, so as the amount of experimental phosphoproteomics data increases, more conserved phosphorylation sites may be revealed... - Protein subfamily assignment using the Conserved Domain DatabaseJessica H Fong
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
BMC Res Notes 1:114. 2008..Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD) that takes into account the organization of the domains into hierarchies of homologous domain models...