Aron Marchler-Bauer

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Annotation of functional sites with the Conserved Domain Database
    Myra 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
  2. pmc Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA
    BMC Bioinformatics 13:144. 2012
  3. pmc CDD: conserved domains and protein three-dimensional structure
    Aron 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
  4. pmc CDD: a Conserved Domain Database for the functional annotation of proteins
    Aron 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
  5. pmc CDD: specific functional annotation with the Conserved Domain Database
    Aron 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
  6. pmc CDD: a conserved domain database for interactive domain family analysis
    Aron 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
  7. pmc CDD: a Conserved Domain Database for protein classification
    Aron 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
  8. pmc CD-Search: protein domain annotations on the fly
    Aron 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
  9. pmc CDD: a curated Entrez database of conserved domain alignments
    Aron 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
  10. pmc CDD: a database of conserved domain alignments with links to domain three-dimensional structure
    Aron 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

Collaborators

Detail Information

Publications25

  1. pmc Annotation of functional sites with the Conserved Domain Database
    Myra 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
    ....
  2. pmc Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
    Andrew F Neuwald
    Institute for Genome Sciences and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA
    BMC Bioinformatics 13:144. 2012
    ..These domain models are annotated to provide insights into the relationships between sequence, structure and function via web-based BLAST searches...
  3. pmc CDD: conserved domains and protein three-dimensional structure
    Aron 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...
  4. pmc CDD: a Conserved Domain Database for the functional annotation of proteins
    Aron 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...
  5. pmc CDD: specific functional annotation with the Conserved Domain Database
    Aron 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
    ....
  6. pmc CDD: a conserved domain database for interactive domain family analysis
    Aron 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...
  7. pmc CDD: a Conserved Domain Database for protein classification
    Aron 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...
  8. pmc CD-Search: protein domain annotations on the fly
    Aron 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...
  9. pmc CDD: a curated Entrez database of conserved domain alignments
    Aron 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...
  10. pmc CDD: a database of conserved domain alignments with links to domain three-dimensional structure
    Aron 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...
  11. pmc MMDB: Entrez's 3D-structure database
    Jie 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...
  12. pmc Database resources of the National Center for Biotechnology Information
    Eric 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...
  13. pmc MMDB: annotating protein sequences with Entrez's 3D-structure database
    Yanli 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)...
  14. pmc IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
    Benjamin 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...
  15. pmc MMDB: Entrez's 3D-structure database
    Yanli 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...
  16. pmc Database resources of the National Center for Biotechnology Information
    Eric 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...
  17. pmc The NCBI BioSystems database
    Lewis 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
    ....
  18. pmc Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
    Benjamin 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...
  19. pmc MMDB: 3D structures and macromolecular interactions
    Thomas 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...
  20. doi request reprint MMDB and VAST+: tracking structural similarities between macromolecular complexes
    Thomas Madej
    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 42:D297-303. 2014
    ..VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure. ..
  21. pmc Database resources of the National Center for Biotechnology Information
    Eric 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...
  22. pmc CORAL: aligning conserved core regions across domain families
    Jessica 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...
  23. ncbi request reprint Comparison of sequence and structure alignments for protein domains
    Aron 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...
  24. pmc Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes
    Viswanadham 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...
  25. pmc Protein subfamily assignment using the Conserved Domain Database
    Jessica 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...