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More papers can be found on individual pages of the lab members
  • Galaktionov, S.G., Tseytin, V.M., Vakser, I.A. et al., 1988, Amphiphilic properties of angiotensin and its fragments, Biophysics, 33:595-598.
  • Galaktionov, S.G., Tseytin, V.M., Vakser, I.A., 1989, Calculation of stable conformations of peptide molecules in a heterogeneous environment, in: Chemistry and Biotechnology of Biologically Active Natural Products, Varna, pp. 302-307.
  • Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 1992, Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques, Proc. Natl. Acad. Sci. USA, 89:2195-2199.
  • Tseytin, V.M., Vakser, I.A., Galaktionov, S.G., 1992, Interaction of peptide and protein molecules with lipophilic environment, in: Modelling and Computer Methods in Molecular Biology and Genetics (Ratner, ed.) Nova Science, New York, pp. 225-230.
  • Vakser, I.A., Aflalo, C., 1994, Hydrophobic docking: A proposed enhancement to molecular recognition techniques, Proteins, 20:320-329.
  • Vakser, I.A., Nikiforovich, G.V., 1995, Protein docking in the absence of detailed molecular structures, in: Methods in Protein Structure Analysis (Atassi & Appella, eds.), Plenum Press, New York, pp. 505-514.
  • Vakser, I.A., 1995, Protein docking for low-resolution structures, Protein Eng., 8:371- 377.
  • Galaktionov, S.G., Tseytin, V.M., Vakser, I.A., Marshall, G.R., 1996, Calculation of peptide orientation at a lipophilic surface: An useful tool for "conformation-function" analysis, in: Peptides: Chemistry, Structure and Biology (Kaumaya, ed.), ESCOM, Leiden, pp. 507-508.
  • Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 1996, The role of geometric fit between protein molecules and their ligands in determining biological specificity, Adv. Molec. Cell Biol., 15B:623-637.
  • Vakser, I.A., 1996, Low-resolution docking: Prediction of complexes for underdetermined structures, Biopolymers, 39:455-464.
  • Vakser, I.A., 1996, Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction, Protein Eng., 9:37-41.
  • Vakser, I.A., 1996, Main-chain complementarity in protein-protein recognition, Protein Eng., 9:741-744.
  • Chang, Y.-T., Stiffelman, O.B., Vakser, I.A., Loew, G.H., Bridges, A., Waskell, L., 1997, Construction of a 3D model of cytochrome P450 2B4, Protein Eng. , 10:119-129.
  • Vakser, I.A., 1997, Evaluation of GRAMM low-resolution docking methodology on hemagglutinin-antibody complex, Proteins, Suppl.1:226-230.
  • Bridges, A., Gruenke, L., Chang, Y.-T., Vakser, I.A., Loew, G., Waskell, L., 1998, Identification of the binding site on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase, J. Biol. Chem., 273:17036-17049.
  • Vakser, I.A., Matar, O.G., Lam, C.F., 1999, A systematic study of low-resolution recognition in protein-protein complexes, Proc. Natl. Acad. Sci. USA , 96:8477-8482.
  • Jiang, S., Vakser, I.A., 2000, Side chains in transmembrane helices are shorter at helix-helix interfaces, Proteins, 40:429-435.
  • Glaser, F., Steinberg, D., Vakser, I.A., Ben-Tal, N., 2001, Residue frequencies and pairing preferences at protein-protein interfaces, Proteins, 43:89-102.
  • Tovchigrechko, A., Vakser, I.A., 2001, How common is the funnel-like energy landscape in protein-protein interactions? Protein Sci., 10:1572-1583.
  • Vakser, I.A., Jiang, S., 2002, Strategies for modeling the interactions of transmembrane helices of G protein-coupled receptors by geometric complementarity using the GRAMM computer algorithm, Methods Enzym., 343:313-328.
  • Vajda, S., Vakser, I.A., Sternberg, M.J.E., Janin, J., 2002, Modeling of protein interactions in genomes, Proteins, 47: 444-446.
  • Tovchigrechko, A., Wells, C.A., Vakser, I.A., 2002, Docking of protein models, Protein Sci., 11:1888-1896.
  • Janin, J., Henrick, K., Moult, J., Ten Eyck, L.F., Sternberg, M.J.E., Vajda, S., Vakser, I.A., Wodak, S.J. 2003, CAPRI: A Critical Assessment of PRedicted Interactions, Proteins, 52:2-9.
  • Jiang, S., Tovchigrechko, A., Vakser, I.A., 2003, The role of geometric complementarity in secondary structure packing: A systematic docking study, Protein Sci., 12: 1646-1651.
  • Jiang, S., Vakser, I.A., 2004, Shorter side chains optimize helix-helix packing, Protein Sci., 13:1426-1429.
  • Vakser, I.A., 2004, Protein-protein interfaces are special, Structure, 12:910-912.
  • Marshall, G.R., Vakser, I.A., 2005, Protein-protein docking methods, in: Proteomics and Protein-Protein Interactions: Biology, Chemistry, Bioinformatics, And Drug Design (G.Waksman, ed.), in press.
  • Tovchigrechko, A., Vakser, I.A., 2005, Development and testing of an automated approach to protein docking, Proteins, 60:296-301.
  • Tovchigrechko, A., Vakser, I.A., 2006, GRAMM-X public web server for protein-protein docking, Nucleic Acids Res, 34:W310-4.
  • Douguet, D., Chen, H.-C., Tovchigrechko, A., and Vakser, I.A., 2006, Dockground resource for studying protein-protein interfaces, Bioinformatics, 22:2612-2618.
  • Nicola, G., Vakser, I.A., 2007, A simple shape characteristic of protein-protein recognition, Bioinformatics, 23:789-792.
  • O'Toole, N., Vakser, I.A., 2007, Large-scale characteristics of the energy landscape in protein-protein interactions, Proteins, in press.
  • Ruvinsky, A.M., Vakser, I.A., 2007, Interaction cutoff effect on ruggedness of protein-protein energy landscape, Proteins, in press.
  • Gao, Y., Douguet, D., Tovchigrechko, A., Vakser, I.A., 2007, DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking, Proteins, in press.
 
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