Thomas Madej

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications18

  1. 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...
  2. 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
    ....
  3. 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...
  4. 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...
  5. 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
    ....
  6. 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...
  7. 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...
  8. 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)...
  9. 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...
  10. 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...
  11. pmc Structural similarity of loops in protein families: toward the understanding of protein evolution
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 5:10. 2005
    ..Structurally aligned protein regions are separated by less conserved loop regions, where sequence and structure locally deviate from each other and do not superimpose well...
  12. 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...
  13. pmc Long-term trends in evolution of indels in protein sequences
    Yuri Wolf
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 7:19. 2007
    ..We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups...
  14. 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
    ....
  15. pmc Evolutionary plasticity of protein families: coupling between sequence and structure variation
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 61:535-44. 2005
    ..Similar sequence-structure analysis performed for protein loop regions shows that evolutionary plasticity of loop regions is greater than for the protein core...
  16. pmc Analysis of protein homology by assessing the (dis)similarity in protein loop regions
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 57:539-47. 2004
    ....
  17. 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...
  18. pmc Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Prog Mol Biol Transl Sci 117:3-24. 2013
    ..In this chapter, we summarize the biological importance of homooligomeric assemblies, physicochemical properties of their interfaces, experimental methods for their identification, their evolution, and role in human diseases...