Chen Yanover

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. pmc M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
    Chen Yanover
    Fred Hutchinson Cancer Research Center, Seattle, WA, USA
    Bioinformatics 25:868-74. 2009
  2. doi request reprint Minimizing and learning energy functions for side-chain prediction
    Chen Yanover
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
    J Comput Biol 15:899-911. 2008
  3. doi request reprint SPRINT: side-chain prediction inference toolbox for multistate protein design
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
    Bioinformatics 26:2466-7. 2010
  4. pmc A computational framework to empower probabilistic protein design
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
    Bioinformatics 24:i214-22. 2008
  5. doi request reprint Design of multispecific protein sequences using probabilistic graphical modeling
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
    Proteins 78:530-47. 2010
  6. doi request reprint Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
    Proteins 75:682-705. 2009
  7. ncbi request reprint Identifying HLA supertypes by learning distance functions
    Tomer Hertz
    School of Computer Science and Engineering, Israel
    Bioinformatics 23:e148-55. 2007
  8. doi request reprint Optimizing energy functions for protein-protein interface design
    Oz Sharabi
    Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
    J Comput Chem 32:23-32. 2011
  9. pmc Large-scale characterization of peptide-MHC binding landscapes with structural simulations
    Chen Yanover
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 108:6981-6. 2011
  10. ncbi request reprint Dead-end elimination for multistate protein design
    Chen Yanover
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
    J Comput Chem 28:2122-9. 2007

Detail Information

Publications13

  1. pmc M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
    Chen Yanover
    Fred Hutchinson Cancer Research Center, Seattle, WA, USA
    Bioinformatics 25:868-74. 2009
    ..Though motif discovery is widely studied and many approaches to it have been suggested, it remains a challenging and as yet unresolved problem...
  2. doi request reprint Minimizing and learning energy functions for side-chain prediction
    Chen Yanover
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
    J Comput Biol 15:899-911. 2008
    ..6%) is obtained using an extended rotamer library and CRF learned weights. Our results suggest that combining machine learning with approximate inference can improve the state-of-the-art in side-chain prediction...
  3. doi request reprint SPRINT: side-chain prediction inference toolbox for multistate protein design
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
    Bioinformatics 26:2466-7. 2010
    ..Finally, SPRINT also has a module for protein side-chain prediction and single-state design. AVAILABILITY: The full C++ source code for SPRINT can be freely downloaded from http://www.protonet.cs.huji.ac.il/sprint...
  4. pmc A computational framework to empower probabilistic protein design
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
    Bioinformatics 24:i214-22. 2008
    ..However, since the number of sequences is exponential in protein length, computational optimization of the distribution is difficult...
  5. doi request reprint Design of multispecific protein sequences using probabilistic graphical modeling
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
    Proteins 78:530-47. 2010
    ..We then compare the approaches of prediction of low energy ensembles and of amino acid profiles and demonstrate their complementarity in providing more robust predictions for protein design...
  6. doi request reprint Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space
    Menachem Fromer
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
    Proteins 75:682-705. 2009
    ....
  7. ncbi request reprint Identifying HLA supertypes by learning distance functions
    Tomer Hertz
    School of Computer Science and Engineering, Israel
    Bioinformatics 23:e148-55. 2007
    ..Recently, a number of computational methods have been proposed for this task. These methods are based on defining protein similarity measures, derived from analysis of binding peptides or from analysis of the proteins themselves...
  8. doi request reprint Optimizing energy functions for protein-protein interface design
    Oz Sharabi
    Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
    J Comput Chem 32:23-32. 2011
    ....
  9. pmc Large-scale characterization of peptide-MHC binding landscapes with structural simulations
    Chen Yanover
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 108:6981-6. 2011
    ....
  10. ncbi request reprint Dead-end elimination for multistate protein design
    Chen Yanover
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
    J Comput Chem 28:2122-9. 2007
    ..We demonstrate the applicability of type-dependent DEE on a set of multistate design problems and discuss its strength and limitations...
  11. pmc Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers
    Chen Yanover
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Nucleic Acids Res 39:4564-76. 2011
    ..The predicted profiles are in good agreement with experimental binding data; furthermore, examination of the modeled structures gives insight into observed binding preferences...
  12. pmc PepDist: a new framework for protein-peptide binding prediction based on learning peptide distance functions
    Tomer Hertz
    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
    BMC Bioinformatics 7:S3. 2006
    ..Representative examples are MHC-peptide complexes in the immune system. Developing computational methods for protein-peptide binding prediction is therefore an important task with applications to vaccine and drug design...
  13. ncbi request reprint HLA mismatches and hematopoietic cell transplantation: structural simulations assess the impact of changes in peptide binding specificity on transplant outcome
    Chen Yanover
    Program in Computational Biology, Fred Hutchinson Cancer Re search Center, Seattle, WA, USA
    Immunome Res 7:24. 2011
    ..This analysis may represent a first step toward sequence-based prediction of relative risk for HLA allele mismatches...