huji Institute of Biochemistry, Food Science and Nutrition

Robert H. Smith Faculty of Agriculture, Food and Environment,
The Hebrew University of Jerusalem

Dr. Masha Niv

Dr. Masha Niv

List of Publications

Articles:

  • Ben-Shimon and Niv Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping PLoS Comput Biol 7(11): e1002288. doi:10.1371/journal.pcbi.1002288 abstract
  • Levit, Yarnitzky, Wiener, Meidan and Niv Modeling of Human Receptors: Interactions with Novel Small-Molecule Binders and Potential Off-Target Drugs. PLoS ONE abstract
  • Wiener, A., Shudler, M., Levit, A. and Niv MY. BitterDB: a database of bitter compounds. (2011) Nucleic Acids Res. abstract,   BitterDB
  • Cheng S, Niv MY, Molecular dynamics simulations and elastic network analysis of protein kinase B (Akt/PKB) inactivation. J Chem Inf Model 2010 Sep;50(9):1602-10. abstract,   PDF
  • Brockhoff A, Behrens M, Niv MY, Meyerhof W. Structural requirements of bitter taste receptor activation. Proc Natl Acad Sci U S A 2010 Jun;1:107(23). abstract,   PDF
  • Yarnitzky T, Levit A, Niv MY. Homology modeling of G-protein-coupled receptors with X-ray structures on the rise. Curr Opin Drug Discov Devel. 2010 May;13(3):317-25. abstract ,  PDF
  • Shudler M, Niv MY. BlockMaster: partitioning protein kinase structures using normal-mode analysis. J Phys Chem A. 2009 Jul 2;113(26):7528-34. abstract ,  PDF
  • Niv, M.Y., Iida, K. Zheng, R., Horiguchi A., Shen, R. and Nanus D.M.
    "Rational Redesign of Neutral Endopeptidase Binding to Merlin and Moesin Proteins", Protein Science. Sci. 2009 May;18(5):1042-50. abstract
  • Rubinstein, M and Niv, M.Y. " Peptidic modulators of protein-protein interactions: Progress and challenges in computational design", Biopolymers, 2009 Jul;91(7):505-1 abstract  PDF
  • Mack E, Ziv E, Reuveni H, Kalman R, Niv MY, Jörns A, Lenzen S, Shafrir E. (2008) Prevention of insulin resistance and beta-cell loss by abrogating PKCepsilon-induced serine phosphorylation of muscle IRS-1 in Psammomys obesus, Diabetes Metab Res Rev. 24:577-584. abstract
  • Madsen KL, Eriksen J, Milan-Lobo L, Han DS , Niv MY, Ammendrup-Johnsen I, Henriksen U, Bhatia VK, Stamou D, Sitte HH, McMahon HT, Weinstein H, Gether U (2008) Membrane Localization is Critical for Activation of the PICK1 BAR Domain, Traffic 9:1327-43. abstract
  • Skrabanek L, Niv M.Y. (2008) Scan2S: Increasing the precision of PROSITE pattern motifs using secondary structure constraints, Proteins 72:1138-1147. abstract  PDF
  • Qvit, N., Reuveni, H., Gazal, S., Peretzman-Shemer, A., Blum, G., Niv, M.Y., Feldstein, A., Meushar, S., Shalev, D.E., Friedler, A. and Gilon, C. (2008) Synthesis of a novel macrocyclic library: discovery of an IGF-1R inhibitor. J Comb Chem. 10:256-66. abstract
  • Niv, M.Y., Skrabanek, L., Roberts, R.J., Scheraga H.A. and Weinstein, H. (2008) Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S-a novel motif scan algorithm with optional secondary structure constraints, Proteins 71:631-40. abstract,  PDF
  • Niv, M.Y. and Filizola, M. (2008) Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis, Proteins 71:575-86. abstract
  • Bargheer, M., Cohen, A., Gerber, R.B., Gühr, M., Korolkov, M.V., Manz, J., Niv, M.Y., Schröder, M. and Schwentner, N., (2007) Dynamics of Electronic States and Spin-Flip for Photodissociation of Dihalogens in Matrices: Experiment, Semiclassical Surface-Hopping and Quantum Models Simulations for F2 and ClF in Solid Ar, J. of Phys. Chem.A. 111:9573-85.

    • Articles published before July 2007:
  • Niv, M.Y., Ripoll, D.R., Vila, J.A., Liwo, A., Vanamee, E.S., Aggarwal, A.K., Weinstein, H. and Scheraga, H.A. (2007) Topology of Type II REases revisited; structural classes and the common conserved core, Nucleic Acids Res. 35:2227-37.   PDF
  • Niv, M.Y., Skrabanek, L., Filizola, M., and Weinstein,H (2006) Structural templates for active state conformations of GPCRs, JCAMD 20: 437-448.   PDF
  • Niv, M.Y. and Weinstein, H. (2005) Flexible docking procedure for the exploration of peptides binding selectivity to PDZ structures and homology models, JACS 127:14072-14079.  PDF
  • Wexler, I.D., Niv, M.Y. and Reuveni, H. (2005) Sequence-based protein kinase inhibition: applications for drug development, Biotechniques 39:575- 576.  PDF
  • Madsen, K., Beuming, T., Niv, M.Y., Chang, V., Dev, K.K., Weinstein, H. and Gether, U. (2005) Molecular determinants for the complex binding specificity of the PDZ domain in PICK1, J. Biol. Chem. 280:20539-20548.  PDF
  • Beuming, T., Skrabanek, L., Niv, M.Y., Murherjee, P. and Weinstein, H. (2005) PDZBase: A protein-protein interaction database for PDZ-domains, Bioinformatics 21:827-828.  PDF
  • Niv, M.Y., Rubin, H., Cohen, J., Tsirulnikov, L., Licht, T., Peretzman- Shemer, A., Cna'an, E., Tartakovsky, A., Stein, I., Albeck, S., Weinstein, I., Goldenberg-Furmanov, M., Tobi, D., Cohen, E., Laster, M., Ben-Sasson, S.A., Reuveni, H. (2004) Sequence-based protein kinase inhibitors applicable for therapeutics and target identification, J. Biol. Chem. 279:1242-1255.  PDF
  • Bargheer, M., Niv, M.Y., Gerber, R.B. and Schwentner, N. (2002) Ultrafast Solvent-Induced Spin-Flip and Non-Adiabatic coupling: ClF in Argon Solids, Phys. Rev. Lett. 89:108301-108304.
  • Cohen, A., Niv, M.Y. and Gerber, R.B. (2001) Formation of novel rare-gas containing molecules by molecular photodissociation in clusters, Faraday Discuss. 118:269-280.
  • Chaban, G., Gerber, R.B., Korolkov, M.V., Manz, J., Niv, M.Y. and B. Schmidt, B. (2001) Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix: Control of Cage Exit Dynamics by Ultrashort Laser Pulses, J.
    of Phys. Chem. A 105:2770-2782.
  • Niv, M.Y., Bargheer, M. and Gerber, R.B. (2000).Photodissociation and Recombination of F2 molecule in Ar54 cluster: Nonadiabatic Molecular Dynamics Simulations, J. Chem. Phys. 113: 6660-6672.
  • Gerber, R.B., Korolkov, M.V., Manz, J., Niv, M.Y. and Schmidt, B. (2000) A reflection principle for the control of molecular photodissociation in solids: Model simulation for F2 in Ar, Chem. Phys. Lett. 327:76-84.
  • Baumfalk, R., Nahler, N.H., Buck, U., Niv, M.Y. and Gerber, R.B. (2000) Photodissociation of HBr adsorbed on the surface and embedded in large Arn clusters, J. Chem. Phys. 113:329-338.
  • Niv, M.Y., Krylov, A.I., Gerber, R.B. and Buck, U. (1999). Photodissociation of HCl adsorbed on Ar12 Cluster: Nonadiabatic Molecular Dynamics Simulations, J. Chem. Phys. 110:11047-11053.
  • Niv, M.Y., Krylov, A. I. and Gerber, R.B. (1997). Photodissociation, Electronic Relaxation and Recombination of HCl in Arn(HCl) Clusters: Nonadiabatic Molecular Dynamics Simulations, Faraday Discussions 108:243-354.

Doctoral Dissertation

"Nonadiabatic transitions in clusters: semiclassical molecular dynamics"
Advisor: Prof. R. Benny Gerber

Patents

M. Y. Niv, U.S. Patent application 60/307,592. Filing date: July 26, 2002. Intermediates for preparation of kinase inhibitors.

M. Y. Niv and D. Tobi, U.S. Patent application 60/311,354. Filing date: August 13, 2002. Compounds that modulate the activity of kinases.

E. Shafrir. E. Ziv, H. Reuveni, M. Niv, U.S. Patent application 60/694,691, Filing date June 29 2005, Prevention of insulin resistance and type 2 diabetes by inhibition of protein kinase C.

 

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