Yanay Ofran

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. ncbi request reprint Create and assess protein networks through molecular characteristics of individual proteins
    Yanay Ofran
    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA
    Bioinformatics 22:e402-7. 2006
  2. ncbi request reprint Predicted protein-protein interaction sites from local sequence information
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
    FEBS Lett 544:236-9. 2003
  3. ncbi request reprint Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Drug Discov Today 10:1475-82. 2005
  4. pmc Protein-protein interaction hotspots carved into sequences
    Yanay Ofran
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
    PLoS Comput Biol 3:e119. 2007
  5. ncbi request reprint ISIS: interaction sites identified from sequence
    Yanay Ofran
    CUBIC and North East Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Bioinformatics 23:e13-6. 2007
  6. ncbi request reprint Prediction of DNA-binding residues from sequence
    Yanay Ofran
    Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
    Bioinformatics 23:i347-53. 2007
  7. ncbi request reprint New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'
    Yana Bromberg
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Curr Opin Drug Discov Devel 12:408-19. 2009
  8. pmc Epitome: database of structure-inferred antigenic epitopes
    Avner Schlessinger
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, Room 804, New York, NY 10032, USA
    Nucleic Acids Res 34:D777-80. 2006
  9. ncbi request reprint Proteins of the same fold and unrelated sequences have similar amino acid composition
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
    Proteins 64:275-9. 2006
  10. ncbi request reprint Analysing six types of protein-protein interfaces
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
    J Mol Biol 325:377-87. 2003

Collaborators

Detail Information

Publications11

  1. ncbi request reprint Create and assess protein networks through molecular characteristics of individual proteins
    Yanay Ofran
    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA
    Bioinformatics 22:e402-7. 2006
    ..Integrating molecular data and insights about the qualities of individual proteins into the analysis may enhance our ability to decipher biological pathways and processes...
  2. ncbi request reprint Predicted protein-protein interaction sites from local sequence information
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
    FEBS Lett 544:236-9. 2003
    ..Incorporating evolutionary and predicted structural information may improve our method. However, even at this early stage, our tool might already assist wet-lab biology...
  3. ncbi request reprint Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Drug Discov Today 10:1475-82. 2005
    ..We shall review the challenges, research approaches and recently developed tools in the field of computational function-prediction and we will discuss the ways these issues can change the process of drug discovery...
  4. pmc Protein-protein interaction hotspots carved into sequences
    Yanay Ofran
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
    PLoS Comput Biol 3:e119. 2007
    ..The server for prediction is available at http://www.rostlab.org/services/isis...
  5. ncbi request reprint ISIS: interaction sites identified from sequence
    Yanay Ofran
    CUBIC and North East Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Bioinformatics 23:e13-6. 2007
    ..Therefore, for the vast majority of proteins, for which there is no high-resolution structure, there is no effective way of identifying interface residues...
  6. ncbi request reprint Prediction of DNA-binding residues from sequence
    Yanay Ofran
    Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
    Bioinformatics 23:i347-53. 2007
    ..Hence, such studies are not applicable on a large scale. If the 3D structure of a protein is known, it is often possible to predict DNA-binding sites in silico. However, for most proteins, such knowledge is not available...
  7. ncbi request reprint New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'
    Yana Bromberg
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Curr Opin Drug Discov Devel 12:408-19. 2009
    ..The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation...
  8. pmc Epitome: database of structure-inferred antigenic epitopes
    Avner Schlessinger
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, Room 804, New York, NY 10032, USA
    Nucleic Acids Res 34:D777-80. 2006
    ..Interactions can be visualized using an interface to Jmol. The database is available at http://www.rostlab.org/services/epitome/...
  9. ncbi request reprint Proteins of the same fold and unrelated sequences have similar amino acid composition
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
    Proteins 64:275-9. 2006
    ..Based on this analysis, we suggest that specific residues that are involved in intramolecular interactions may account for this surprising relationship between composition and structure...
  10. ncbi request reprint Analysing six types of protein-protein interfaces
    Yanay Ofran
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
    J Mol Biol 325:377-87. 2003
    ..Overall, our results suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications...
  11. ncbi request reprint Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
    Jason A Greenbaum
    Immune Epitope Database and Analysis Resource IEDB, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    J Mol Recognit 20:75-82. 2007
    ..By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools...