Dina SCHENIDMAN


EDUCATION
     Tel-Aviv University                                                                                                2008
     Ph.D. in Computer Science
     Thesis: Algorithms for Prediction of Molecular Interactions.
     Thesis advisors: Prof. Haim Wolfson and Prof. Ruth Nussinov


     Tel-Aviv University                                                                                                2003
     M.Sc. in Computer Science, magna cum laude
     Thesis: Unbound Docking of Rigid Molecules.
     Thesis advisors: Prof. Haim Wolfson and Prof. Ruth Nussinov


     Tel-Aviv University                                                                                                 1998
     B.Sc. double major in Computer Science and Mathematics


EMPLOYMENT
School of Computer Science and Engineering and Institute of Life Sciences                                          2016-Present
Hebrew University of Jerusalem                                                                                                               
Senior Lecturer.


Department of Biopharmaceutical Sciences, University of California San Francisco                               2008-2015
Postdoc fellow in Andrej Sali lab. Development and application of algorithms for integrative structural modeling.


Ramot, Pharmalogica Consortium, Tel-Aviv University                                                                             2001-2003
Research Assistant.
Development of algorithms for prediction of drug metabolism by Cytochrome P450 enzymes.


IDF, ISRAEL                                                                                                                                               1998-2001
Project Supervisor.
Management and coordination of military projects in cooperation with civilian companies.


PROFESSIONAL ACTIVITIES
Software Editor, PLOS Comp. Biol.                                                                                                        2015-Present
Associate Editor, BMC Struct Biol.                                                                                                         2012-Present
Program Committee Member Research in Comp. Mol. Biol. (RECOMB)                                              2014
Manuscript referee for the following journals and conference proceedings: Bioinformatics,                 2003-Present
Biopolymers, BMC Bioinformatics, IEEE T. Pattern Anal., J. Biomol. Struct. Dyn.,
J. Chem. Inf. Model., J. Comput.-Aided Mol. Des., J. Math. Model. Algorithms, J.
Mol. Graphics Model., J. Struct Biol., Nucleic Acids Res., PLoS One, Proteins, Structure,
Research in Comp. Mol. Biol. (RECOMB) and European Conf. on Comp. Biol. (ECCB).
Blog about peer review:
http://crosstalk.cell.com/blog/recognizing-peer-review-and-peer-reviewers
Participation in Critical Assessment of PRediction of Interactions (CAPRI) - community                      2001-present
wide experiment on the comparative evaluation of protein-protein docking.

 

AWARDS
FISEB (ILANIT), Travel Fellowship                                                                                                                   2014
Weizmann Institute of Science, National Postdoctoral Award Program for Advancing Women in Science     2008
EMBO Long Term Fellowship for Post doctoral studies in Europe (declined)                                                  2008
Marejn Award for excellence in Ph.D. studies                                                                                                  2007
Wolf Fellowship for excellence in Ph.D. studies                                                                                               2005
Deutch Award for excellence in M.Sc. studies                                                                                                  2003


SELECTED PUBLICATIONS

  1. Lensink MF, Velankar S, Kryshtafovych A, Huang S, Schneidman-Duhovny D, Sali A et al. (2016) Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins, 84:323–348.
  2. Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A (2013) Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics 29:3158-66.
  3. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Vel ́azquez-Muriel J, Strop P, Liang H, Krukenberg K, Liao M, Kim HM, Sobhanifar S, D ̈otsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A (2012) A method for integrative structure determination of protein-protein complexes. Bioinformatics 28:3282-3289.
  4. Russel D, Lasker K, Webb B, Vel ́azquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A (2012) Putting the pieces together: integrative modeling plat-form software for structure determination of macromolecular assemblies. PLoS Biol. 10:e1001244.
  5. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33:W363-367.
  6. (Schneidman) Duhovny D, Nussinov R, Wolfson HJ (2002) Efficient unbound dock-ing of rigid molecules. Proceedings of the 2nd Workshop on Algorithms in Bioinfor-matics (WABI) LNCS 2452, pp. 185-200, Springer Verlag.

SOFTWARE AND SERVERS

  1. PatchDock server - a method for fast rigid unbound docking of molecules. 60K jobs, 1000 downloads per year
  2. FireDock server - an efficient method for refinement and re-scoring of rigid-body protein-protein docking solutions. 25K jobs, 200 downloads per year
  3. FoXS server - a method for fast SAXS profile computation with Debye formula. 15K jobs, 300 downloads per year
  4. SymmDock server - a method for prediction of complexes with cyclic symmetry by geometry based docking.
  5. PharmaGist server - a method for pharmacophore detection.
  6. HingeProt server - a method for protein hinge prediction using Normal Mode Analysis.
  7. FoXSDock server - a method for docking with SAXS profile.
  8. FlexDock - a method for flexible docking with hinge motion.
  9. MultiFoXS server - a method for multi-state modeling with SAXS profiles.