Victor Zharavin

Post-doc

 

TUM Weihenstephan

          Room: OG-L09

Phone: +49(0)8161 71 2132

Email: v.zharavin@tum.de

 

                                                                                                                                                                                                                                            

Personal data


 

  • Since June 2015 Scientist (postdoc) at the Department of Genome Oriented Bioinformatics
  • 2013-2015 Researcher, development of methods of sparse data processing and analysis,  SNC/Gothenburg University and Bruker Biospin, Karlsruhe, Germany
  • 2008-2013 Research Group Leader, FP7 project ‘WeNMR’ – bioinformatics and system biology, Biozentrum/BMRZ, Goethe University, Frankfurt a.M., Germany
  • 2004-2008 Sr. Researcher, FP6 project ‘extend-NMR’ - computational methods in biomolecular NMR, SNC/Gothenburg University, Göteborg, Sweden
  • 1998-2004 Sr. Researcher, biomolecular protein sciences, Biozentrum, Department of Structural Biology, Basel University, Switzerland
  • 1994-1998 PhD Researcher, development of computational methods for novel types of pharmaceutics for heart diseases therapy, Institute of Bioorganic Chemistry, Moscow, Russia
  • 1990-1994 Scientist, R&D on Computer Science and Artificial Intelligence methods, Space Research Institute, Moscow, Russia
  • 1983-1989 Study of Physics/Biophysics (B.Sc./M.Sc.) at Moscow Institute of Physics and Technology, Russia

 

 

Research interests


  

  • Genomics & Proteomics: bioinformatics of epitopes for immunotherapy of cancers using transcriptomics & proteomics data; prediction of flexibility of large membrane proteins using machine learning and other methods of bioinformatics
  • Protein structure, folding, dynamics and protein-ligand interactions

  • MDD- and NMF-based methods of sparse nD-data processing

 

 
Publications


 §   Jaravine V., Tikole S. (2015) “Calculation of NMR and EPR Parameters: Theory and Application”, Koros Press.  

§   Orekhov, V.Y., Jaravine, V.A. (2011). “Analysis of NUS Spectra with MDD.” Progress NMR Spec, 59, 271-292.

§   Jaravine, V., Ibraghimov, I., and Orekhov, V.Y. (2006). “Removal of a Time Barrier for High-Resolution Multidimensional NMR Spectroscopy.” In Nature: Milestones in Spin, Nature Publishing Group.

§   Grzesiek, S., Cordier, F., Jaravine, V., and Barfield, M. (2004). “Insights into Biomolecular Hydrogen Bonds from Hydrogen Bond Scalar Couplings.” Progress NMR, 45, 275-300.

§   Dingley, A.J., Cordier, F., Jaravine, V., and Grzesiek, S. (2003). “Scalar Couplings Across Hydrogen Bonds.” In BioNMR in Drug Research, Z. Oliver, ed. (Wiley-VCH Verlag), pp. 207-226.

§   Tikole S, Jaravine V, Rogov V, Dötsch V, Güntert P. “Peak picking NMR spectral data using non-negative matrix factorization.” (2014) BMC Bioinformatics, 15:46.

§   Tikole S, Jaravine V, Orekhov VY, Güntert P. “Effects of NMR spectral resolution on protein structure calculation.” (2013) PLoS One, 8:e68567.

§   Bagaria A, Jaravine V, Güntert P. “Estimating structure quality trends in the Protein Data Bank by equivalent resolution”. (2013) Comput Biol Chem 46:8-15.

§   Bagaria A., Jaravine V., Huang Y.J., Montelione G.T., Güntert P. “Protein Structure Validation by GLM-RMSD prediction.” (2012) Protein Science 21, 229-38.

§   Tikole S., Jaravine V., Rogov V.V., Rozenknop A., Schmöe K., Löhr F., Dötsch V., Güntert P. “Faster than Death: NMR of Short-Lived Biosamples.” (2012) ChemBioChem, 13, 967-7.

§   Rogov V.V., Rozenknop A., Rogova N., Löhr F., Zharavin V., Tikole S., Güntert P, Dikic I., Dötsch V. “NMR-Compatible Expression Tag Provides New Perspectives in the Study Of Proteins And Their Interactions.” (2012) ChemBioChem, 13, 959-63.

§   Rosato A, …, Jaravine V, et al. “Blind testing of routine, fully automated determination of protein structures from NMR data.” (2012) Structure, Cell-Press 20:227-36.

§   Wassenaar, T.A., Dijk, M.V., Ferreira, N.L., Schot, G.V., Vries, S.J., Zwan, J.V., Boelens, R., Giachetti, A., Carotenuto, D., Jaravine, V., et al. (2011). "e-NMR: Structural Biology on the Grid.” Structural bioinformatics, accepted.

§   Ferreira, N.L., Wassenaar, T.A., Vries, S.J., Dijk, M., Schot, G., Zwan, J., Boelens, R., Giachetti, A., Bagaria, A., Zharavin, V., et al. (2010). “e-NMR Grid-Enabled Infrastructure.” Computacion,360-80.

§   Wong, L.E., Masse, J.E., Jaravine, V., Orekhov, V., and Pervushin, K. (2008). “Automatic Assignment of Protein Backbone Resonances by Direct Spectrum Inspection in Targeted Acquisition of NMR Data.” J Biomol NMR 42, 77-86.

§   Jaravine, V.A., Zhuravleva, A.V., Permi, P., Ibraghimov, I., and Orekhov, V.Y. (2008). “Hyperdimensional NMR Spectroscopy with Nonlinear Sampling.” J Am Chem Soc 130, 3927-3936.

§   Jaravine, V.A., and Orekhov, V.Y. (2006). “Targeted acquisition for real-time NMR spectroscopy.” J Am Chem Soc 128, 13421-13426.

§   Jaravine, V., Ibraghimov, I., and Orekhov, V.Y. (2006). “Removal of a Time Barrier for High-Resolution Multidimensional NMR Spectroscopy.” Nat Methods 3, 605-607.

§   Luan, T., Jaravine, V., Yee, A., Arrowsmith, C.H., and Orekhov, V.Y. (2005). “Optimization of Resolution and Sensitivity of 4D NOESY using Multi-Dimensional Decomposition.” J Biomol NMR 33, 1-14.

§   Jaravine, V., and Grzesiek, S. (2004). “Quantifying Hydrogen Bonding to Solvent from Amide Chemical Shifts During TFE-Induced Peptide Folding.” In J Biomol NMR, pp. unpubl.manuscript.

§   Bocharov, E.V., Sobol, A.G., Pavlov, K.V., Korzhnev, D.M., Jaravine, V.A., Gudkov, A.T., and Arseniev, A.S. (2004). “From structure and dynamics of protein L7/L12 to molecular switching in ribosome.” J Biol Chem 279, 17697-17706.

§   Jaravine, V.A., Cordier, F., and Grzesiek, S. (2004). “Quantification of H/D isotope effects on protein hydrogen-bonds by h3JNC' and 1JNC' couplings and peptide group 15N and 13C chemical shifts.” J Biomol NMR 29, 309-318.

§   Kammerer, R.A., Jaravine, V.A., Frank, S., Schulthess, T., Landwehr, R., Lustig, A., Garcia-Echeverria, C., Alexandrescu, A.T., Engel, J., and Steinmetz, M.O. (2001). “An Intrahelical Salt Bridge within the Trigger Site Stabilizes the GCN4 Leucine Zipper.” J Biol Chem 276, 13685-13688.

§   Jaravine, V.A., Alexandrescu, A.T., and Grzesiek, S. (2001). “Observation of the Closing of Individual Hydrogen Bonds During TFE-Induced Helix Formation in a Peptide.” Protein Sci 10, 943-950.

§   Alexandrescu, A.T., Lamour, F.P., and Jaravine, V.A. (2000). “NMR evidence for progressive stabilization of native-like structure upon aggregation of acid-denatured LysN.” J Mol Biol 295, 239-255.

§   Jaravine, V.A., Rathgeb-Szabo, K., and Alexandrescu, A.T. (2000). “Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide.” Protein Sci 9, 290-301.

§   Utkin, I.N., Dubovskii, P.V., Dubinnyi, M.A., Zharavin, V.A., Simonova, T.N., Barsukov, L.I., and Arsen'ev, A.S. (1999a). “Lys35 spin-labeled cytotoxin II from Naja oxiana venom for study of its interaction with phospholipid membranes by EPR.” Bioorg Khim 25, 930-932.

§   Utkin, Y.N., Dubovskii, P.V., Dubinnyi, M.A., Zharavin, V.A., Simonova, T.N., Barsukov, L.I., and Arseniev, A.S. (1999b). “The Naja Oxiana Venom Cytotoxin II Spin-Labeled at Lys35 for the EPR Study of its Interaction With Phospholipid Membranes.” Bioorg Khim 25, 930-932.

§   Alexandrescu, A.T., Jaravine, V.A., Dames, S.A., and Lamour, F.P. (1999). “NMR Hydrogen Exchange of the OB-Fold Protein Lysn as a Function Of Denaturant: The Most Conserved Elements of Structure Are The Most Stable to Unfolding.” J Mol Biol 289, 1041-1054.

§   Golovanov, A.P., Efremov, R.G., Jaravine, V.A., Vergoten, G., Kirpichnikov, M.P., and Arseniev, A.S. (1998). “A New Method to Characterize Hydrophobic Organization of Proteins: Application to Rational Protein Engineering of Barnase.” J Biomol Struct Dyn 15, 673-687.

§   Jaravine, V.A., Golovanov, A.P., and Arseniev, A.S. (1997a). “The Rational Evolution of Scorpion Toxins.” Bioorg Khim 23, 710-720.

§   Jaravine, V.A., Nolde, D.E., Reibarkh, M.J., Korolkova, Y.V., Kozlov, S.A., Pluzhnikov, K.A., Grishin, E.V., and Arseniev, A.S. (1997b). “Three-Dimensional Structure of Toxin OSK1 from Orthochirus Scrobiculosus Scorpion Venom.” Biochemistry 36, 1223-1232.

§   Golovanov, A.P., Efremov, R.G., Jaravine, V.A., Vergoten, G., and Arseniev, A.S. (1995). “Amino Acid Residue: is it Structural Or Functional?” FEBS Lett 375, 162-166.

§   Zharavin, V., and Usikoff, D. (1989a). “Image Recognition for Automated Vehicle Navigation.” SRI Proc.

§   Zharavin, V., and Usikoff, D. (1989b). “Scene Analysis Module of the Mars Pathfinder.” SRI Proc.

§   Zharavin, V., Shapiro, V., and Galeev, A. (1988). “Modelling Effect Of High-Energy Beam on Cold Plasma With A System Of Differential Equations.” SRI Proc.

§   Zharavin, V., Shapiro, V., and Galeev, A. (1987). “Ray-Tracing Model Of Propagation Of Plasmons In Near Space.” SRI Proc.