Alexandra Shulman-Peleg

Summary

Affiliation: Tel Aviv University
Country: Israel

Publications

  1. pmc SiteEngines: recognition and comparison of binding sites and protein-protein interfaces
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 33:W337-41. 2005
  2. pmc Spatial chemical conservation of hot spot interactions in protein-protein complexes
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv 69978, Israel
    BMC Biol 5:43. 2007
  3. pmc Prediction of interacting single-stranded RNA bases by protein-binding patterns
    Alexandra Shulman-Peleg
    School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    J Mol Biol 379:299-316. 2008
  4. pmc MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 36:W260-4. 2008
  5. ncbi request reprint The multiple common point set problem and its application to molecule binding pattern detection
    Maxim Shatsky
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Israel
    J Comput Biol 13:407-28. 2006
  6. pmc Structural similarity of genetically interacting proteins
    Oranit Dror
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv, 69978, Israel
    BMC Syst Biol 2:69. 2008
  7. ncbi request reprint Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design
    Oranit Dror
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Curr Med Chem 11:71-90. 2004
  8. ncbi request reprint From structure to function: methods and applications
    Haim J Wolfson
    School of Computer Science, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Curr Protein Pept Sci 6:171-83. 2005
  9. ncbi request reprint Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
    Shira Mintz
    Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
    Proteins 61:6-20. 2005
  10. pmc RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 37:D369-73. 2009

Detail Information

Publications12

  1. pmc SiteEngines: recognition and comparison of binding sites and protein-protein interfaces
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 33:W337-41. 2005
    ..The methods are highly efficient and the freely available software packages are suitable for large-scale database searches of the entire PDB...
  2. pmc Spatial chemical conservation of hot spot interactions in protein-protein complexes
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv 69978, Israel
    BMC Biol 5:43. 2007
    ..Due to the lack of computational tools for recognition of spatial patterns of interactions shared by a set of protein-protein complexes, the conservation of such interactions has not been addressed previously...
  3. pmc Prediction of interacting single-stranded RNA bases by protein-binding patterns
    Alexandra Shulman-Peleg
    School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    J Mol Biol 379:299-316. 2008
    ....
  4. pmc MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 36:W260-4. 2008
    ..The input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the shared interaction properties of the interfaces...
  5. ncbi request reprint The multiple common point set problem and its application to molecule binding pattern detection
    Maxim Shatsky
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Israel
    J Comput Biol 13:407-28. 2006
    ..We show applications of MultiBind to several biological targets. The method recognizes patterns which are responsible for binding small molecules, such as estradiol, ATP/ANP, and transition state analogues...
  6. pmc Structural similarity of genetically interacting proteins
    Oranit Dror
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University, Tel Aviv, 69978, Israel
    BMC Syst Biol 2:69. 2008
    ..To date, less than 2% of the known genetic interactions in yeast or worm can be accounted for by sequence similarity...
  7. ncbi request reprint Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design
    Oranit Dror
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Curr Med Chem 11:71-90. 2004
    ..In particular, we present the framework of the algorithms, classify their modules and point out their advantages and challenges...
  8. ncbi request reprint From structure to function: methods and applications
    Haim J Wolfson
    School of Computer Science, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Curr Protein Pept Sci 6:171-83. 2005
    ..We hope the review will lead to a broader utilization of computational methods, and their cross-fertilization with experiment...
  9. ncbi request reprint Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
    Shira Mintz
    Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
    Proteins 61:6-20. 2005
    ..We expect that these would yield further information regarding the forces stabilizing protein-protein interactions...
  10. pmc RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases
    Alexandra Shulman-Peleg
    School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 37:D369-73. 2009
    ..This database is accessible at http://bioinfo3d.cs.tau.ac.il/RsiteDB...
  11. ncbi request reprint Recognition of functional sites in protein structures
    Alexandra Shulman-Peleg
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    J Mol Biol 339:607-33. 2004
    ..We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions...
  12. ncbi request reprint Interaction of c(60)-fullerene and carboxyfullerene with proteins: docking and binding site alignment
    Hadar Benyamini
    Bioinformatics Unit, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Bioconjug Chem 17:378-86. 2006
    ..A high similarity between the physicochemical properties and surface geometry was found for fullerene's binding sites of HIV protease and the human and bovine serum albumins...