Igor B Kuznetsov

Summary

Affiliation: University at Albany
Country: USA

Publications

  1. pmc PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids
    Igor B Kuznetsov
    Cancer Research Center and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, 12144, USA
    BMC Res Notes 8:187. 2015
  2. pmc FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins
    Igor B Kuznetsov
    GenNY sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA
    Bioinformation 3:134-6. 2008
  3. pmc Protein sequence alignment with family-specific amino acid similarity matrices
    Igor B Kuznetsov
    Cancer Research Center, Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, USA 12144
    BMC Res Notes 4:296. 2011
  4. ncbi request reprint Simplified computational methods for the analysis of protein flexibility
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, One Discovery Drive, Rensselaer, NY 12144, USA
    Curr Protein Pept Sci 10:607-13. 2009
  5. pmc A web server for inferring the human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, One Discovery Drive, Rensselaer, NY 12144, USA
    Bioinformatics 25:1185-6. 2009
  6. doi request reprint ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA
    Bioinformatics 24:1534-5. 2008
  7. doi request reprint Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data
    Igor B Kuznetsov
    Department of Epidemiology and Biostatistics, Gen NY Sis Center for Excellence in Cancer Genomics, University at Albany, Rensselaer, New York 12144, USA
    Proteins 72:74-87. 2008
  8. ncbi request reprint Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, Rensselaer, NewYork 12144, USA
    Proteins 64:19-27. 2006
  9. ncbi request reprint A novel sensitive method for the detection of user-defined compositional bias in biological sequences
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, State University of New York One Discovery Drive, Rensselaer, NY 12144, USA
    Bioinformatics 22:1055-63. 2006
  10. pmc Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations
    Igor B Kuznetsov
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
    Protein Sci 13:3230-44. 2004

Collaborators

Detail Information

Publications16

  1. pmc PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids
    Igor B Kuznetsov
    Cancer Research Center and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, 12144, USA
    BMC Res Notes 8:187. 2015
    ..Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities...
  2. pmc FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins
    Igor B Kuznetsov
    GenNY sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA
    Bioinformation 3:134-6. 2008
    ..If a PDB file is submitted, then the web-server uses sequence-derived information and residue solvent accessibility calculated from this file...
  3. pmc Protein sequence alignment with family-specific amino acid similarity matrices
    Igor B Kuznetsov
    Cancer Research Center, Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, USA 12144
    BMC Res Notes 4:296. 2011
    ..This work is focused on the issue of finding optimized protein family- and fold-specific scoring functions for global similarity matrix-based sequence alignment...
  4. ncbi request reprint Simplified computational methods for the analysis of protein flexibility
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, One Discovery Drive, Rensselaer, NY 12144, USA
    Curr Protein Pept Sci 10:607-13. 2009
    ....
  5. pmc A web server for inferring the human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, One Discovery Drive, Rensselaer, NY 12144, USA
    Bioinformatics 25:1185-6. 2009
    ..The web server can be used for a fast determination of NAT2 phenotypes in genetic screens...
  6. doi request reprint ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA
    Bioinformatics 24:1534-5. 2008
    ..In the case of novel proteins that lack functional annotation, statistically significant CBS reported by ProBias can be used to guide the search for potential functionally important sites or domains...
  7. doi request reprint Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data
    Igor B Kuznetsov
    Department of Epidemiology and Biostatistics, Gen NY Sis Center for Excellence in Cancer Genomics, University at Albany, Rensselaer, New York 12144, USA
    Proteins 72:74-87. 2008
    ..Application of the present methodology to the prion protein (PrP) shows that conformationally variable positions predicted in its ordered C-terminal domain are located within segments presumed to be involved in refolding of PrP...
  8. ncbi request reprint Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, Rensselaer, NewYork 12144, USA
    Proteins 64:19-27. 2006
    ..A web-server implementation of the predictors is freely available online at http://lcg.rit.albany.edu/dp-bind/...
  9. ncbi request reprint A novel sensitive method for the detection of user-defined compositional bias in biological sequences
    Igor B Kuznetsov
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, University at Albany, State University of New York One Discovery Drive, Rensselaer, NY 12144, USA
    Bioinformatics 22:1055-63. 2006
    ..A detailed large-scale analysis of the functional implications and evolutionary conservation of different compositionally biased segments requires a sensitive method capable of detecting user-specified types of compositional bias...
  10. pmc Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations
    Igor B Kuznetsov
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
    Protein Sci 13:3230-44. 2004
    ..We suggest that the observed increase in hydrophobicity may facilitate PrP-to-PrP or/and PrP-to-cofactor interactions, and thus promote structural conversion...
  11. ncbi request reprint DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
    Seungwoo Hwang
    Gen NY Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA
    Bioinformatics 23:634-6. 2007
    ..AVAILABILITY: Freely available at http://lcg.rit.albany.edu/dp-bind. SUPPLEMENTARY INFORMATION: http://lcg.rit.albany.edu/dp-bind/dpbind_supplement.html...
  12. ncbi request reprint Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors
    Igor B Kuznetsov
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA
    Proteins 54:333-41. 2004
    ..These results suggest that intrinsic structural propensities may be an important determinant of the rate of folding in small two-state proteins...
  13. pmc On the properties and sequence context of structurally ambivalent fragments in proteins
    Igor B Kuznetsov
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA
    Protein Sci 12:2420-33. 2003
    ..These results have implications for protein design and structure prediction...
  14. ncbi request reprint Similarity between the C-terminal domain of the prion protein and chimpanzee cytomegalovirus glycoprotein UL9
    Igor B Kuznetsov
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, Box 1023, One Gustave L Levy Place, New York, NY 10029, USA
    Protein Eng 16:861-3. 2003
    ....
  15. ncbi request reprint Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading
    Igor B Kuznetsov
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA
    Proteins 49:266-84. 2002
    ..For each potential, our methodology is able to identify a potential-specific amino acid distance matrix and a reduced amino acid alphabet of any specified size, which may have implications for sequence alignment and multibody models...
  16. pmc CFP: a web-server for constructing sequence-based protein conformational flexibility profiles
    Igor B Kuznetsov
    Cancer Research Center, Department of Epidemiology and Biostatistics, University at Albany, One Discovery Drive, Rensselaer, NY 12144, USA
    Bioinformation 4:176-8. 2009
    ..The statistical significance of a flexible sequence segment is assessed using the discrete scan statistics based on the density of flexible residues observed in this segment...