Barak Raveh

Department of Bioengineering and Therapeutic Sciences
1700 4th Street
Byers Hall, Suite BH501, Mission Bay Campus
University of California, San Francisco
San Francisco, CA 94158-2330


barak at
Research Interests

I am developing and applying methods for the integrative modeling of complex biological processes, focusing primarily on the nucleocytoplasmic transport system, which regulates the high-volume molecular traffic between the nucleus and the cytoplasm through the coordinated function of nuclear pore complexes (NPCs) and various nuclear transport factors. To uncover the fundamental biophysical principles through which the transport system functions both efficiently and selectively, it is necessary to integrate diverse types of experimental and theoretical data, obtained using a wide array of experimental, computational and theoretical methods. The data for modeling such complex biological system is typically acquired at multiple levels of spatial and temporal resolutions, and therefore I take special interest in pursuing a multi-scale modeling approach that enables seamless integration of such heterogeneous data.

Select Publications
  • Simple rules for passive diffusion through the nuclear pore complex
    Timney BL*, Raveh B*, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP (2016) Journal of Cell Biology pdf
  • Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex
    Raveh B*, Karp JM*, Sparks S*, Dutta K, Rout MP, Sali A, Cowburn D (2016) Proceedings of the National Academy of Sciences
  • 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
  • A little more, a lot better: Improving path quality by a simple path merging algorithm.
    Raveh B, Enosh A, and Halperin D (2011) IEEE Transactions on Robotics
  • Sub-angstrom modeling of complexes between flexible peptides and globular proteins.
    Raveh B*, London N*, and Furman-Schueler O. Raveh B*, Enosh A,Furman-Schueler O and Halperin D (2009) PLOS Computational Biology 5(2): e1000295
    Selected for Resarch Highlights track, ISMB/ECCB 2009, Stockholm
  • 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) Biophysical Journal 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
    Awarded Best Student Paper 2nd prize, ECCB 2006, Eilat
  • * equal contribution
Reviews and book chapters
  • Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how.
    London N, Raveh B, Schueler-Furman O (2013) Curr Opin Struct Biol 23(6):894-902.
  • Druggable protein-protein interactions – from hot spots to hot segments.
    London N, Raveh B, Schueler-Furman O (2013) Curr Opin Chem Biol 17(6):952-959.
  • Modeling peptide protein interactions.
    Lonon N, Raveh B, Schueler-Furman O (2012) Methods Mol Biol. 857:375-98.