Supervisors:
Dr. Ora Schueler-Furman, Dept. of Molecular Genetics and Biotechnology, Hadassah Medical School, The Hebrew University.
Dan Halperin, Laboratory of Applied Computation Biology, School of Computer Science, Tel-Aviv University

• Peptide-Protein Interactions:
  Short flexible peptides mediate key regulatory interactions in the cell. Together with Nir London and Lior Zimmerman, we have developed Rosetta FlexpepDock, a computational modeling tool for accurate modelling of peptide-protein complex structures. We also studied the possibility to drive short inhibitory peptides from interfaces of globular proteins.
• Protein Motion and Motion Planning:
  The dynamic conformational changes of proteins are key to understanding their function. Using motion-planning techniques inspired by robotics algorithms, we study large-scale molecular motion, with the aim of bridging experimental observation and computational techniques.
• Planning high-quality motion paths:
  Combining theory and practice, I study the problem of finding high-quality motion paths (with respect to path length, energy, etc.) when moving an object with many degrees of freedom in an environment clattered with obstacles.

• Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.
  Raveh B, London N, Zimmerman L and Furman-Schueler O (2011) PLoS ONE (special Rosetta collection issue).
• Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the α-kinase domain.
  Crawley SW, Gharaei MS, Ye Q, Yang Y, Raveh B, London N, Schueler-Furman O, Jia Z, Côté GP (2011) Journal of Biological Chemistry
• Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions. London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O (2011) Nucleic Acids Research
• A little more, a lot better: Improving path quality by a simple path merging algorithm.
  Raveh B, Enosh A, and Halperin D (2011) IEEE Trans Robotics
• Sub-angstrom modeling of complexes between flexible peptides and globular proteins.
  Raveh B*, London N*, and Furman-Schueler O. (2010) Proteins 78(9):2029-2040.
• Rapid sampling of molecular motions with partial information constraints. Raveh B*, Enosh A,Furman-Schueler O and Halperin D (2009) PLOS Comp Biol 5(2): e1000295.
• Generation, comparison and merging of pathways between protein conformations: Gating in K-channels.
  Enosh A., Raveh B., Furman-Schueler O., Halperin D., and Ben-Tal N. (2008) Biophys J 95:3850-3860.
• Rediscovering secondary structures as network motifs – an unsupervised learning approach.
  Raveh B.*, Rahat O*., Basri R. Schreiber G. (2007) Bioinformatics 23: e163-e169.
• Predicting metal binding sites from APO protein structures.
  Babor M., Gerzon S., Raveh B., Sobolev V. and Edelman M. (2007) Proteins 70(1):208-17.
* equal contribution

• Flexible Peptide Docking.
  The 6th Conference of Rosetta Developers in Leavenworth, Washington, USA, 2009.
• Rapid sampling of molecular motion with prior information constraints: Insights into channel gating and domain swapping.
  ISMB/ECCB 2009, Stockholm, Sweden, 2009.
  Presented in the Resarch Highlights track (by Ora Schueler-Furman)
• Structural Modeling of Peptides that Fold upon Binding to a Globular Partner.
  EMBO Practical Course on Docking Predictions of Protein-Protein Interactions, Barcelona, Spain, 2008.
• PathRover: sampling dynamic molecular motion with Rosetta.
  The 5th Conference of Rosetta Developers in Leavenworth, Washington, USA, 2008.
• Rediscovering Secondary Structures as Network Motives – an Unsupervised Learning Approach.
  European Conference of Computational Biology (ECCB) 2006, Eilat, Israel.
  Receipient of Best Student Paper Award, 2nd prize.

Barak Raveh
Department of Molecular Genetics and Biotechnology,
Medical Research Institute, Hadassh Medical School
The Hebrew University in Jerusalem

• Mail: barak.raveh at mail.huji.ac.il
• Phone (Ein-Karem): 02-6757063
• Phone (Tel-Aviv): 03-6406114