Dr. Dror Tobi

Publications

Papers

2011 - Current

Tobi D. (2018) “Dynamics based clustering of globin family members.” PLoS One. Dec 4;13(12):e0208465.

Aharoni R, Tobi D., (2018) “Dynamical comparison between Myoglobin and Hemoglobin.” Proteins. 2018 Sep 5. doi: 10.1002/prot.25598.

Taussig R. D., Tobi D., Zwilling M. (2018) “The importance of timing in estimating beta” Eurasian Econ. Rev. https://doi.org/10.1007/s40822-018-0103-7.

Tobi D. (2017)Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method.” Proteins 85(8):1507-1517.

Redko B, Tuchinsky H, Segal T, Tobi D, Luboshits G, Ashur-Fabian O, Pinhasov A, Gerlitz G, Gellerman G. (2017) “Toward the development of a novel non-RGD cyclic peptide drug conjugate for treatment of human metastatic melanoma.” Oncotarget. 8(1):757-768.

Yacobovich S, Tuchinsky L, Kirby M, Kardash T, Agranyoni O, Nesher E, Redko B, Gellerman G, Tobi D., Gurova K, Koman I, Ashur Fabian O, Pinhasov A. (2016) “Novel synthetic cyclic integrin αvβ3 binding peptide ALOS4: Antitumor activity in mouse melanoma models.” Oncotarget 7(39):63549-63560.

Tobi D. (2016) “Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain” Proteins 84:267-77.

Tobi D. (2014) “Normal Mode Dynamics Comparison of Proteins.” Isr. J. Chem., 54: 1118–1125.

Davis M, Tobi D. (2014) ” Multiple Gaussian network modes alignment reveals dynamically variable regions: the hemoglobin case.” Proteins 82(9):2097-105.

Tobi D. (2013) “Large scale analysis of the dynamics of enzymes” Proteins 81(11) 1910-18.

Tobi D. (2012) “Dynamics alignment: Comparison of protein dynamics in the SCOP database” Proteins 80(4):1167-76.

2001 - 2010

Tobi D. (2010) “Designing Coarse Grained- and Atom based- Potentials for Protein-protein Docking” BMC Struct Biol, 10:40.

Cohavi O, Tobi D, Schreiber G. (2009) “Docking of antizyme to ornithine decarboxylase and antizyme inhibitor using experimental mutant and double-mutant cycle data” J Mol Biol. 390:503-515.

Bahar I, Chennubhotla C, Tobi D. (2007) “Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation.” Curr. Opin. Struct. Biol. 17:633-40.

Tobi D. and Bahar I. (2007) “Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?”, BMC Bioinformatics 2007, 8:226.

Tobi D. and Bahar I. (2006) “Optimal Design of Protein Docking Potentials: Efficiency and Limitations” Proteins: Structure, Function, and Bioinformatics62 970-981.

Tobi D. and Bahar I. (2005) “Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State”, Proc. Natl. Acad. Sci. (U S A), 102 18908-18913.

John K. Vries,  Rajan Munshi, Dror Tobi, Judith Klein-Seetharaman, Panayiotis V. Benos, Ivet Bahar (2004)  “A Sequence Alignment-Independent Method For Protein Classification” Applied Bioinformatics 3(2-3) 137-148.

Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A, Tobi D, Bahar I, Stephenson C.R, Wipf P, Lazo J.S. (2004) “Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase” Mol. Pharmacol. 66(4) 824-833.

Niv MY, 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 SA, Reuveni H. (2004) “Sequence-based design of kinase inhibitors applicable for therapeutics and target identification.” J. Biol. Chem. 279(2) 1242-1255.

Xu C, Tobi D, Bahar I. (2003) “Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<–>R2 transition”, J. Mol. Biol. 333(1) 153-68.

Tobi D, Elber R, Thirumalai D. (2003) “The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study”, Macromolecules, 68(3) 359-69.

2000 and before

Tobi D, Elber R. (2000) “Distance-Dependent, Pair Potential for Protein Folding: Results from Linear Optimization”, Proteins, 41,40-46.

Tobi D, Shafran G, Linial N, Elber R.  (2000) “On the design and analysis of protein folding potentials”, Proteins 40, 71-85.

Keasar C, Tobi D, Elber R, Skolnick J.  (1998) “Coupling the folding of homologous proteins”, PNAS, 95, 5880-5883.

Tobi D, Wiser O, Trus M, Atlas D. (1998) “N-type voltage-sensitive calcium channel interact with syntaxin, synaptotagmin and SNAP-25 in a multiprotein complex”, RECEPTORS & CHANNELS, 6, 89-98.

Wiser O, Tobi D, Trus M, Atlas D. (1997) “Synaptotagmin restores kinetic properties of a syntaxin–associated N-type voltage sensitive calcium channel”, FEBS LETTERS, 404, 203-207 1997.

Wiser O, Trus M, Tobi D, Halevi S, Giladi E, Atlas D. (1996)  “The alpha 2/delta subunit of voltage sensitive Ca2+ channels is a single transmembrane extracellular protein which is involved in regular secretion”, FEBS LETTERS, 379, 15-20.

Book Chapters

Esposito E.X, Tobi D, and Madura J.D. (2006) “The Methods and Implementation of Comparative Protein Modelling”, in “Reviews in Computational Chemistry, volume 22” Kenny B. Lipkowitz, Thomas R. Cundari, and Valerie J. Gillet, John Wiley & Sons, Inc. 57-168.