Stephen H Bryant

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint A structure-based method for protein sequence alignment
    Maricel G Kann
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
    Bioinformatics 21:1451-6. 2005
  2. pmc PubChem3D: conformer ensemble accuracy
    Sunghwan Kim
    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 5:1. 2013
  3. pmc Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
    Sunghwan Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, 20894, MD, USA
    J Cheminform 4:28. 2012
  4. pmc Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge
    Viswanadham Sridhara
    National Library of Medicine, NIH, Bethesda, Maryland, USA
    Proteome Sci 10:8. 2012
  5. pmc Automated annotation of chemical names in the literature with tunable accuracy
    Jun 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
  6. pmc PubChem3D: Biologically relevant 3-D similarity
    Sunghwan Kim
    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 3:26. 2011
  7. pmc PubChem3D: Shape compatibility filtering using molecular shape quadrupoles
    Sunghwan Kim
    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 3:25. 2011
  8. pmc PubChem3D: Diversity of shape
    Evan E Bolton
    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 3:9. 2011
  9. pmc PubChem3D: Similar conformers
    Evan E Bolton
    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 3:13. 2011
  10. pmc PubChem3D: Conformer generation
    Evan E Bolton
    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 3:4. 2011

Detail Information

Publications73

  1. ncbi request reprint A structure-based method for protein sequence alignment
    Maricel G Kann
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
    Bioinformatics 21:1451-6. 2005
    ....
  2. pmc PubChem3D: conformer ensemble accuracy
    Sunghwan Kim
    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 5:1. 2013
    ..abstract:..
  3. pmc Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
    Sunghwan Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, 20894, MD, USA
    J Cheminform 4:28. 2012
    ..abstract:..
  4. pmc Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge
    Viswanadham Sridhara
    National Library of Medicine, NIH, Bethesda, Maryland, USA
    Proteome Sci 10:8. 2012
    ..abstract:..
  5. pmc Automated annotation of chemical names in the literature with tunable accuracy
    Jun 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:..
  6. pmc PubChem3D: Biologically relevant 3-D similarity
    Sunghwan Kim
    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 3:26. 2011
    ..abstract:..
  7. pmc PubChem3D: Shape compatibility filtering using molecular shape quadrupoles
    Sunghwan Kim
    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 3:25. 2011
    ..abstract:..
  8. pmc PubChem3D: Diversity of shape
    Evan E Bolton
    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 3:9. 2011
    ..abstract:..
  9. pmc PubChem3D: Similar conformers
    Evan E Bolton
    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 3:13. 2011
    ..abstract:..
  10. pmc PubChem3D: Conformer generation
    Evan E Bolton
    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 3:4. 2011
    ..abstract:..
  11. pmc The PubChem chemical structure sketcher
    Wolf D Ihlenfeldt
    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 1:20. 2009
    ..It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects...
  12. pmc The Text-mining based PubChem Bioassay neighboring analysis
    Lianyi Han
    National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    BMC Bioinformatics 11:549. 2010
    ..In this work, we propose a text-mining based approach for bioassay neighboring analysis from the unstructured text descriptions contained in the PubChem BioAssay database...
  13. pmc Database resources of the National Center for Biotechnology Information
    David 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...
  14. 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 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...
  15. pmc An overview of the PubChem BioAssay resource
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D255-66. 2010
    ..In this work, we describe the PubChem BioAssay database, including data model, bioassay deposition and utilities that PubChem provides for searching, downloading and analyzing the biological activity information contained therein...
  16. 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
    ....
  17. 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...
  18. pmc Database resources of the National Center for Biotechnology Information
    David 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...
  19. 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...
  20. pmc Database resources of the National Center for Biotechnology Information
    David 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...
  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 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. pmc Homology inference of protein-protein interactions via conserved binding sites
    Manoj Tyagi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e28896. 2012
    ....
  27. 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...
  28. 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
    ....
  29. 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)...
  30. 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...
  31. pmc PubChem's BioAssay Database
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D400-12. 2012
    ..In this work, we provide an update for the PubChem BioAssay resource, including information content growth, data model extension and new developments of data submission, retrieval, analysis and download tools...
  32. pmc Knowledge-based annotation of small molecule binding sites in proteins
    Ratna R Thangudu
    National Center for Biotechnology Information, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    BMC Bioinformatics 11:365. 2010
    ..To benefit from the rapidly increasing structural data, it is essential to improve the tools that enable large scale binding site prediction with greater emphasis on their biological validity...
  33. pmc State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 7:499. 2006
    ..Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis...
  34. pmc Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins
    Thomas Madej
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Struct Biol 7:23. 2007
    ..Along with these we also consider the "gapped structural alignment score" (GSAS), which was introduced earlier by other researchers...
  35. 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...
  36. 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...
  37. 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...
  38. pmc The identification of complete domains within protein sequences using accurate E-values for semi-global alignment
    Maricel G Kann
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:4678-85. 2007
    ..When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance...
  39. pmc Exploring functional roles of multibinding protein interfaces
    Manoj Tyagi
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Protein Sci 18:1674-83. 2009
    ....
  40. pmc Finding biologically relevant protein domain interactions: conserved binding mode analysis
    Benjamin A Shoemaker
    Computational Biology Branch, National Center for Biotechnology Information, Building 38A, National Institutes of Health, Bethesda, MD 20894, USA
    Protein Sci 15:352-61. 2006
    ..The method's ability to sort through and classify large numbers of putative interacting domain pairs is demonstrated on the oligomeric interactions of globins...
  41. 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...
  42. pmc Refining multiple sequence alignments with conserved core regions
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:2598-606. 2006
    ..A standalone version of the program is available by ftp distribution (ftp://ftp.ncbi.nih.gov/pub/REFINER) and will be incorporated into the next release of the Cn3D structure/alignment viewer...
  43. 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...
  44. pmc Improving protein structure similarity searches using domain boundaries based on conserved sequence information
    Kenneth Evan Thompson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Struct Biol 9:33. 2009
    ....
  45. 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...
  46. pmc CDART: protein homology by domain architecture
    Lewis 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...
  47. 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
    ....
  48. pmc FSelector: a Ruby gem for feature selection
    Tiejun Cheng
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 28:2851-2. 2012
    ..FSelector also provides many useful auxiliary tools, including normalization, discretization and missing data imputation...
  49. pmc PubChem3D: a new resource for scientists
    Evan E Bolton
    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 3:32. 2011
    ..abstract:..
  50. pmc A comparison of position-specific score matrices based on sequence and structure alignments
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Protein Sci 11:361-70. 2002
    ..We discuss these observations, and suggest a strategy for constructing seed alignments that optimize PSSM-sequence alignment accuracy and recognition sensitivity...
  51. pmc Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors
    Zhigang Zhou
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    J Mol Graph Model 30:135-47. 2011
    ..The multi-conformation method to build 3D QSAR is very effective approach to obtain satisfactory models with high correlation with experimental results and high prediction power for unknown compounds...
  52. pmc Functional states of homooligomers: insights from the evolution of glycosyltransferases
    Kosuke Hashimoto
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A 8S814, Bethesda, MD 20894, USA
    J Mol Biol 399:196-206. 2010
    ....
  53. pmc Modulating protein-protein interactions with small molecules: the importance of binding hotspots
    Ratna Rajesh Thangudu
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    J Mol Biol 415:443-53. 2012
    ..We investigate possible mechanisms of how small molecules may modulate protein-protein binding and discuss examples of new candidates for drug design...
  54. pmc Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Chem Inf Model 51:229-36. 2011
    ..Moreover, our work may be used for comparative evaluation of solubility classification studies ascribe to the use of completely public resources...
  55. pmc Structure-based virtual screening for drug discovery: a problem-centric review
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    AAPS J 14:133-41. 2012
    ....
  56. pmc Functional specificity lies within the properties and evolutionary changes of amino acids
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 373:801-10. 2007
    ..Extensive benchmarking by comparing the performance of SPEER with other specificity site prediction algorithms has shown that it performs better in predicting several categories of subfamily specific sites...
  57. pmc QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules
    Zhigang Zhou
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Graph Model 28:714-27. 2010
    ....
  58. pmc Database resources of the National Center for Biotechnology Information
    David 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 33:D39-45. 2005
    ..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...
  59. pmc A novel method for mining highly imbalanced high-throughput screening data in PubChem
    Qingliang Li
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 25:3310-6. 2009
    ....
  60. pmc Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex
    Zhigang Zhou
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland 20894, USA
    J Comput Chem 30:2165-75. 2009
    ..Our results also show that the results based on protein dimer show better correlations with experimental activity when compared to results based on monomer in the in silico calculations...
  61. pmc Modeling the evolution of protein domain architectures using maximum parsimony
    Jessica 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...
  62. ncbi request reprint Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry
    Ming 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...
  63. 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...
  64. pmc PubChem: a public information system for analyzing bioactivities of small molecules
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:W623-33. 2009
    ..Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually...
  65. ncbi request reprint State of the art: refinement of multiple sequence alignments
    Saikat Chakrabarti
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 11:3. 2010
    ..ABSTRACT: Correction to Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH: State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006, 7:499...
  66. ncbi request reprint Open mass spectrometry search algorithm
    Lewis 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...
  67. pmc PubChem as a public resource for drug discovery
    Qingliang Li
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Drug Discov Today 15:1052-7. 2010
    ..As a public resource, PubChem lowers the barrier for researchers to advance the development of chemical tools for modulating biological processes and drug candidates for disease treatments...
  68. 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...
  69. pmc Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
    J Chem Inf Model 51:2440-8. 2011
    ..Furthermore, BASS identified a significant fraction of structurally diverse compounds with similar bioactivities, indicating its feasibility of "scaffold hopping" in searching novel molecules against the target of interest...
  70. pmc Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem
    Lianyi Han
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 9:401. 2008
    ..Computational approaches for the analysis of HTS results face great challenges due to the large quantity of information and significant amounts of erroneous data produced...
  71. pmc Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules
    Tiejun Cheng
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 26:2881-8. 2010
    ....
  72. pmc A survey of across-target bioactivity results of small molecules in PubChem
    Lianyi Han
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 25:2251-5. 2009
    ..This work enables one to select target specific inhibitors, identify promiscuous compounds and better understand the biological mechanisms of target-small molecule interactions...
  73. ncbi request reprint Outcome of a workshop on archiving structural models of biological macromolecules
    Helen M Berman
    The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
    Structure 14:1211-7. 2006