Research Topics
| Lewis Y GeerSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
|
Detail Information
Publications
Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor chargeViswanadham Sridhara
National Library of Medicine, NIH, Bethesda, Maryland, USA
Proteome Sci 10:8. 2012..abstract:..- Automated annotation of chemical names in the literature with tunable accuracyJun D Zhang
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Cheminform 3:52. 2011..abstract:.. - 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 InformationDavid L Wheeler
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 35:D5-12. 2007..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - 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 37:D5-15. 2009..Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - Database resources of the National Center for Biotechnology InformationDavid L Wheeler
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 36:D13-21. 2008..Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - 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... - 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... - 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: 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... - 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... - 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)... - 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 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... 
DBParser: web-based software for shotgun proteomic data analysesXiaoyu Yang
National Institutes of Health, 10 Center Drive, Room 3D42, Bethesda, Maryland 20892-1262, USA
J Proteome Res 3:1002-8. 2004..DBParser actively links to the primary mass spectral data and to public online databases such as NCBI, GO, and Swiss-Prot in order to structure contextually specific reports for biologists and biochemists...- 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... - 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... - 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: 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... - Database resources of the National Center for Biotechnology InformationDavid L Wheeler
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 34:D173-80. 2006..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov... - CDART: protein homology by domain architectureLewis Y Geer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Genome Res 12:1619-23. 2002..Searches can be further refined by taxonomy and by selecting domains of interest. CDART is available at http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi... - 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... - Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometryMing Xu
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
J Proteome Res 4:300-5. 2005..Many spectra examined that do not have significant matches are assessed to have good spectral quality, indicating that advances in search methods may yield substantial improvements in results... - Open mass spectrometry search algorithmLewis Y Geer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
J Proteome Res 3:958-64. 2004..At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets... - Modeling the evolution of protein domain architectures using maximum parsimonyJessica H Fong
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
J Mol Biol 366:307-15. 2007..Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function... - 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...