B.S. in Biology, 1994, Magna Cum Laude, Hebrew University, Jerusalem, Israel

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1 Dror Tobi Curriculum Vitae Department of Computer Sciences and Mathematics phone: Ariel University Center of Samaria fax: Ariel drorto@ariel.ac.il Israel EDUCATION Ph.D. in Biochemistry, 2003, Hebrew University, Jerusalem, Israel Adviser: Prof. Ron Elber Thesis: Enhancements and Applications of Theoretical Approaches to Predict Protein Structures. M.S. in Biochemistry, 1996, Magna Cum Laude, Hebrew University, Jerusalem, Israel Adviser: Prof. Daphne Atlas Thesis: Interactions of Synaptic Proteins with Calcium Channels. B.S. in Biology, 1994, Magna Cum Laude, Hebrew University, Jerusalem, Israel PROFESSIONAL APPOINTMENTS 2009 Present Senior Lecturer Department of Computer Sciences and Mathematics, Department of Molecular Biology, Ariel University Center of Samaria. Teaching: Bioinformatics, Structural Biology, and Programming courses. Research: Designing protein-protein docking potentials. Developing protein annotation algorithms Lecturer Department of Computer Sciences and Mathematics, Department of Molecular Biology, Ariel University Center of Samaria. Teaching: Bioinformatics, Structural Biology, and Programming courses. Research: Designing protein-protein docking potentials. Developing protein annotation algorithms Research Associate Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA Supervisor: Ivet Bahar Investigating protein dynamics using coursed-grained elastic network models and atomic scale simulation in order to understand structure and function. Calculated dynamics of unbound complex monomers to infer the role of induced fit and conformational selection as mechanisms for protein-protein binding. Studied Dror Tobi CV Page 1

2 Hemoglobin dynamics to understand the T R2 transition. Designed protein-protein docking potentials using linear-programming technique. Developing a protein-protein docking program. Analyzing sequences n-grams frequencies, and the correlation of unique n-grams to proteins functionally important sites. Modeling and virtual screening of small molecule inhibitors to human CDC25B, work in collaboration with Dr. John Lazo Bioinformatics Researcher KERYX Biopharmaceuticals, Jerusalem, Israel Designed small molecule drugs using SYBYL (TRIPOS) modules. Calculated proteins structure using the Homology Modeling technique. Performed sequence analysis of protein kinase families. Performed molecular dynamic simulations. Development of a novel algorithm for drug design Teaching Assistant Department of Biological Chemistry, Hebrew University, Jerusalem, Israel Taught recitations for Ph.D., graduate and undergraduate students in biochemistry and computational biology. Developed quiz questions, directed laboratory experiments, met with students upon requests, and graded written work Research Assistant Department of Biological Chemistry, Hebrew University, Jerusalem, Israel Supervisor: Ron Elber Improved an algorithm for coupled folding of homologous proteins on lattice. Designed coarse grained potentials for protein folding using a linear programming technique, which became part of the LOOPP program ( Performed molecular dynamic simulations to understand the denaturing effect of urea on proteins Research Assistant Department of Biological Chemistry, Hebrew University, Jerusalem, Israel Supervisor: Daphne Atlas Expressed proteins in E. coli; purified proteins on affinity columns. Preformed protein binding experiments on columns and two-hybrid system experiments. HONORS AND AWARDS Teaching Assistant's Scholarship from the Institute of Life Sciences, Hebrew University of Jerusalem 1996 M.SC in Biochemistry, magna cum laude 1994 B.SC in Biology, magna cum laude 1992 Cited in Dean s register of outstanding students Dror Tobi CV Page 2

3 Research Grants ISF grant "Developing potentials for protein docking and binding sites recognition" 140,000NIS/year. Publications 17. Cohavi O, Tobi D, Schreiber G. (2009) Docking of antizyme to ornithine decarboxylase and antizyme inhibitor using experimental mutant and doublemutant cycle data J Mol Biol. 390: Bahar I, Chennubhotla C, Tobi D. (2007) Intrinsic Dynamics of Proteins: Functionality and Biological Implications Curr. Opin. Struct. Biol. 17: Tobi D. and Bahar I. (2007) Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?, BMC Bioinformatics 2007, 8: Tobi D. and Bahar I. (2006) Optimal Design of Protein Docking Potentials: Efficiency and Limitations Proteins: Structure, Function, and Bioinformatics, Esposito E.X, Tobi D, and Madura J.D. (2006) The Methods and Implementation of Comparative Protein Modelling, in Reviews in Computational Chemistry, volume 22 Kenny B. Lipkowitz, Thomas R. Cundari, and Valerie J. Gillet, John Wiley & Sons, Inc Tobi D. and Bahar I. (2005) Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State, Proc. Natl. Acad. Sci. (U S A), John K. Vries, Rajan Munshi, Dror Tobi, Judith Klein-Seetharaman, Panayiotis V. Benos, Ivet Bahar (2004) A Sequence Alignment-Independent Method For Protein Classification Applied Bioinformatics 3(2-3) Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A, Tobi D, Bahar I, Stephenson C.R, Wipf P, Lazo J.S. (2004) Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase Mol. Pharmacol. 66(4) Dror Tobi CV Page 3

4 9. Niv MY, Rubin H, Cohen J, Tsirulnikov L, Licht T, Peretzman-Shemer A, Cna'an E, Tartakovsky A, Stein I, Albeck S, Weinstein I, Goldenberg-Furmanov M, Tobi D, Cohen E, Laster M, Ben-Sasson SA, Reuveni H. (2004) Sequence-based design of kinase inhibitors applicable for therapeutics and target identification. J. Biol. Chem. 279(2) Xu C, Tobi D, Bahar I. (2003) Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition, J. Mol. Biol. 333(1) * 7. Tobi D, Elber R, Thirumalai D. (2003) The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study, Macromolecules, 68(3) Tobi D, Elber R. (2000) Distance-Dependent, Pair Potential for Protein Folding: Results from Linear Optimization, Proteins, 41, ** 5. Tobi D, Shafran G, Linial N, Elber R. (2000) On the design and analysis of protein folding potentials, Proteins 40, ** 4. Keasar C, Tobi D, Elber R, Skolnick J. (1998) Coupling the folding of homologous proteins, PNAS, 95, Tobi D, Wiser O, Trus M, Atlas D. (1998) N-type voltage-sensitive calcium channel interact with syntaxin, synaptotagmin and SNAP-25 in a multiprotein complex, RECEPTORS & CHANNELS, 6, Wiser O, Tobi D, Trus M, Atlas D. (1997) Synaptotagmin restores kinetic properties of a syntaxin associated N-type voltage sensitive calcium channel, FEBS LETTERS, 404, Wiser O, Trus M, Tobi D, Halevi S, Giladi E, Atlas D. (1996) The alpha 2/delta subunit of voltage sensitive Ca 2+ channels is a single transmembrane extracellular protein which is involved in regular secretion, FEBS LETTERS, 379, ** Cited more then 50 times * Cited more then 30 times Invited Talks Dror Tobi CV Page 4

5 5. Structural Changes Involved in Protein Binding Correlate with Intrinsic Motions of Proteins in the Unbound State, Biophysical theory club, University of Pittsburgh, Pittsburgh PA, March Structural Changes Involved in Protein Binding Correlate with Intrinsic Motions of Proteins in the Unbound State, The 3 rd Annual Biological Language Conference, Carnegie Mellon University, Pittsburgh PA, November 28-29, Structural Changes Involved in Protein Binding Correlate with Intrinsic Motions of Proteins in the Unbound State, Computational Studies of Proteins Workshop, University of Cincinnati, Cincinnati, OH, September 8, CDC25A / NSC Docking Model, Molecular-to-Cellular Modeling of Complex Biological Processes workshop, University of Pittsburgh, Pittsburgh PA, February 3, The use of 4-grams for Protein Classification and Sequence Comparison, 2 nd Biological Language Modeling Workshop, Carnegie Mellon University, Pittsburgh PA, May TECHNICAL COURSES Protein Modeling Techniques (Tripos, Inc.) Introduction to Structure-Based Design (Tripos, Inc.) Virtual Screening (Tripos, Inc.) TECHNICAL SKILLS Programming languages: C/C++, FORTRAN, Perl, HTML. Modeling: SYBYL (Tripos Inc.), MEO (Chemical Computing Group Inc.), Gold (Cambridge Crystallographic Data Centre), Silver (Cambridge Crystallographic Data Centre). Molecular dynamics: MOIL, GROMACS. Protein visualization: PyMol, Swiss-PDB-Viewer, Rasmol. AFFILIATIONS International Society for Computational Biology RESEARCH INTERESTS My research has encompassed a broad range of interests including: primary sequence analysis; molecules dynamics using both coarse-grain and atomic scale techniques; protein folding studies using the Monte Carlo algorithm; designing potentials for protein Dror Tobi CV Page 5

6 folding and protein-protein docking; characterization of the mechanisms of protein complexes formation; modeling drug candidates in a protein active site. My current research efforts are directed towards understanding protein dynamics and molecular recognition which are of fundamental importance to drug design and biotechnology. My future research will include (i) Improving current computational approaches for rational drug design. (II) Development novel computational tools to assist in designing drugs capable of blocking protein-protein interaction sites. Such tools do not currently exit and are of great need. (iii) Use of network models to understand protein-protein interactions and protein folding. (iv) Combining coarse-grain and atomic scale protein dynamics techniques. Dror Tobi CV Page 6