Valentin A Ilyin

Summary

Affiliation: Northeastern University
Country: USA

Publications

  1. pmc TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
    Chesley M Leslin
    Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
    Nucleic Acids Res 35:D317-21. 2007
  2. pmc Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
    Alper Uzun
    Department of Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
    Nucleic Acids Res 35:W384-92. 2007
  3. ncbi request reprint ModView, visualization of multiple protein sequences and structures
    Valentin A Ilyin
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Bioinformatics 19:165-6. 2003
  4. pmc Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
    Valentin A Ilyin
    Biology Department, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
    Protein Sci 13:1865-74. 2004
  5. ncbi request reprint Friend, an integrated analytical front-end application for bioinformatics
    Alexej Abyzov
    Department of Biology, Northeastern University, Boston, MA, USA
    Bioinformatics 21:3677-8. 2005
  6. pmc MODBASE, a database of annotated comparative protein structure models
    Ursula Pieper
    Laboratories of Molecular Biophysics, The Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 30:255-9. 2002
  7. ncbi request reprint Structural exon database, SEDB, mapping exon boundaries on multiple protein structures
    Chesley M Leslin
    Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
    Bioinformatics 20:1801-3. 2004
  8. ncbi request reprint LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures
    Ashley C Stuart
    Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Bioinformatics 18:200-1. 2002
  9. pmc An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces
    Alexej Abyzov
    Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 4:e1000066. 2008
  10. pmc A comprehensive analysis of non-sequential alignments between all protein structures
    Alexej Abyzov
    Department of Biology, Northeastern University 360 Huntington Avenue, Boston, MA 02115, USA
    BMC Struct Biol 7:78. 2007

Collaborators

Detail Information

Publications12

  1. pmc TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
    Chesley M Leslin
    Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
    Nucleic Acids Res 35:D317-21. 2007
    ..T-DB presents researchers with the opportunity for comprehensive studies of the variability in proteins and is publicly available at http://mozart.bio.neu.edu/topofit/index.php...
  2. pmc Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
    Alper Uzun
    Department of Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
    Nucleic Acids Res 35:W384-92. 2007
    ..The server is publicly available at http://glinka.bio.neu.edu/StSNP/...
  3. ncbi request reprint ModView, visualization of multiple protein sequences and structures
    Valentin A Ilyin
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Bioinformatics 19:165-6. 2003
    ..ModView is also suitable as a graphical interface to various databases because it can be controlled through JavaScript commands and called from CGI scripts...
  4. pmc Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
    Valentin A Ilyin
    Biology Department, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
    Protein Sci 13:1865-74. 2004
    ..The TOPOFIT method also helps to detect conformational changes, topological differences in variable parts, which are particularly important for studies of variations in active/ binding sites and protein classification...
  5. ncbi request reprint Friend, an integrated analytical front-end application for bioinformatics
    Alexej Abyzov
    Department of Biology, Northeastern University, Boston, MA, USA
    Bioinformatics 21:3677-8. 2005
    ..The application is linked and communicates with local and remote sequence and structure databases...
  6. pmc MODBASE, a database of annotated comparative protein structure models
    Ursula Pieper
    Laboratories of Molecular Biophysics, The Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 30:255-9. 2002
    ....
  7. ncbi request reprint Structural exon database, SEDB, mapping exon boundaries on multiple protein structures
    Chesley M Leslin
    Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
    Bioinformatics 20:1801-3. 2004
    ..AVAILABILITY: SEDB is publicly available at http://glinka.bio.neu.edu/SEDB/SEDB.html SUPPLEMENTARY INFORMATION: On the SEDB Web site...
  8. ncbi request reprint LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures
    Ashley C Stuart
    Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Bioinformatics 18:200-1. 2002
    ..Residues in the binding sites are graphically depicted for comparison with other structurally defined family members. LigBase provides a resource for the analysis of families of related binding sites...
  9. pmc An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces
    Alexej Abyzov
    Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 4:e1000066. 2008
    ..The method described here can be used for analysis in any DNA-metabolizing pathway where weak interactions are the principal mode of cross-talk among participants and co-crystal structures of the individual components are available...
  10. pmc A comprehensive analysis of non-sequential alignments between all protein structures
    Alexej Abyzov
    Department of Biology, Northeastern University 360 Huntington Avenue, Boston, MA 02115, USA
    BMC Struct Biol 7:78. 2007
    ..We present here a comprehensive large-scale study of non-sequential alignments between available protein structures in Protein Data Bank...
  11. pmc Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis
    Alper Uzun
    Department of Biology, Northeastern University, Boston, MA, USA
    BMC Genomics 10:183. 2009
    ..The objectives of this study were to determine transcript abundance of HMGN3a and SMARCAL1 in mature bovine oocytes and early bovine embryos, to perform comparative functional genomics analysis of these genes across mammals...
  12. pmc Tools for comparative protein structure modeling and analysis
    Narayanan Eswar
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 31:3375-80. 2003
    ....