Barak Raveh, PhD

TitleAssociate Specialist
InstitutionUniversity of California San Francisco
Address1700 4th St
San Francisco CA 94158
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    NPCs dot the nuclear envelope of every eukaryotic cells and form a selective barrier for molecular transport between the cytoplasm and the nucleus. In my research, I am working to create a data-driven model of transport through nuclear pore complexes (NPCs). For this end, I am developing and applying tools for modeling spatio-temporal systems based on multiple sources of experimental data, at multiple levels of spatial and temporal resolutions.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. Integrative structure and functional anatomy of a nuclear pore complex. Nature. 2018 Mar 22; 555(7697):475-482. PMID: 29539637.
      View in: PubMed
    2. Ziarek JJ, Kleist AB, London N, Raveh B, Montpas N, Bonneterre J, St-Onge G, DiCosmo-Ponticello CJ, Koplinski CA, Roy I, Stephens B, Thelen S, Veldkamp CT, Coffman FD, Cohen MC, Dwinell MB, Thelen M, Peterson FC, Heveker N, Volkman BF. Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation. Sci Signal. 2017 Mar 21; 10(471). PMID: 28325822.
      View in: PubMed
    3. Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. Simple rules for passive diffusion through the nuclear pore complex. J Cell Biol. 2016 Oct 10; 215(1):57-76. PMID: 27697925.
      View in: PubMed
    4. Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci U S A. 2016 May 03; 113(18):E2489-97. PMID: 27091992; PMCID: PMC4983827 [Available on 11/03/16].
    5. Raveh B. A backdoor to the nucleus that runs in the family? Structure. 2014 Dec 02; 22(12):1693-1694. PMID: 25470426.
      View in: PubMed
    6. Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. Modeling of proteins and their assemblies with the Integrative Modeling Platform. Methods Mol Biol. 2014; 1091:277-95. PMID: 24203340.
      View in: PubMed
    7. London N, Raveh B, Schueler-Furman O. Druggable protein-protein interactions--from hot spots to hot segments. Curr Opin Chem Biol. 2013 Dec; 17(6):952-9. PMID: 24183815.
      View in: PubMed
    8. London N, Raveh B, Schueler-Furman O. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr Opin Struct Biol. 2013 Dec; 23(6):894-902. PMID: 24138780.
      View in: PubMed
    9. London N, Raveh B, Schueler-Furman O. Modeling peptide-protein interactions. Methods Mol Biol. 2012; 857:375-98. PMID: 22323231.
      View in: PubMed
    10. London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O. Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W249-53. PMID: 21622962; PMCID: PMC3125795.
    11. Raveh B, London N, Zimmerman L, Schueler-Furman O. Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One. 2011 Apr 29; 6(4):e18934. PMID: 21572516; PMCID: PMC3084719.
    12. Buch I, Fishelovitch D, London N, Raveh B, Wolfson HJ, Nussinov R. Allosteric regulation of glycogen synthase kinase 3ß: a theoretical study. Biochemistry. 2010 Dec 28; 49(51):10890-901. PMID: 21105670; PMCID: PMC3005830.
    13. London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O. Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins. 2010 Nov 15; 78(15):3140-9. PMID: 20607702; PMCID: PMC2952690.
    14. Crawley SW, Gharaei MS, Ye Q, Yang Y, Raveh B, London N, Schueler-Furman O, Jia Z, Côté GP. Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the alpha-kinase domain. J Biol Chem. 2011 Jan 28; 286(4):2607-16. PMID: 21071445; PMCID: PMC3024756.
    15. Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins. 2010 Jul; 78(9):2029-40. PMID: 20455260.
      View in: PubMed
    16. Raveh B, Enosh A, Schueler-Furman O, Halperin D. Rapid sampling of molecular motions with prior information constraints. PLoS Comput Biol. 2009 Feb; 5(2):e1000295. PMID: 19247429; PMCID: PMC2637990.
    17. Enosh A, Raveh B, Furman-Schueler O, Halperin D, Ben-Tal N. Generation, comparison, and merging of pathways between protein conformations: gating in K-channels. Biophys J. 2008 Oct; 95(8):3850-60. PMID: 18621834; PMCID: PMC2553149.
    18. Babor M, Gerzon S, Raveh B, Sobolev V, Edelman M. Prediction of transition metal-binding sites from apo protein structures. Proteins. 2008 Jan 01; 70(1):208-17. PMID: 17657805.
      View in: PubMed
    19. Raveh B, Rahat O, Basri R, Schreiber G. Rediscovering secondary structures as network motifs--an unsupervised learning approach. Bioinformatics. 2007 Jan 15; 23(2):e163-9. PMID: 17237086.
      View in: PubMed
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