Publications

  1. T.J.Taylor, I.I.Vaisman 
    Graph theoretic properties of networks formed by the Delaunay tessellation of protein structures.  
    Phys. Rev. E, 2006. 73, 4, p. xxxx.

  2. M.Masso, Z.Lu, I.I.Vaisman 
    Computational mutagenesis studies of protein structure-function correlations. 
    Proteins, 2006 (in press)
    3. [Medline]

  3. E.Mathe, M.Olivier, S.Kato, C.Ishioka, I.I.Vaisman, P.Hainaut 
    Predicting the transactivation activity of p53 Missense Mutants Using a Four-Body Potential Score Derived from Delaunay Tessellations. 
    Human Mutation, 2006, 27, 2, 163-172.
    4. [Medline]

  4. M.Barenboim, D.C.Jamison, I.I.Vaisman 
    A Statistical Geometry Approach to the Study of Functional Effects of Human Non-synonymous SNPs. 
    Human Mutation, 2005, 26, 5, 471-476.
    5. [Medline]

  5. T.Taylor, M.Rivera, G.Wilson, I.I.Vaisman 
    New method for protein secondary structure assignment based on a simple topological descriptor. 
    Proteins, 2005, 60, 3, 513-524.  [Medline]

  6. T.Pushkarsky, V.Yurchenko, C.Vanpouille, B.Brichacek, I.I.Vaisman, S.Hatakeyama, K.I.Nakayama, B.Sherry, M.I.Bukrinsky. 
    Cell surface expression of CD147/EMMPRIN is regulated by cyclophilin 60. 
    J Biol Chem., 2005, 280, 30, 27866-27871. [Medline]

  7. D.L.Bostick, M.Shen, I.I.Vaisman  
    A simple topological representation of protein structure: implications for new, fast, and robust structural classification.  
    Proteins, 2004, 56, 3, 487-501. [Medline]

  8. I.I.Vaisman 
    Statistical and computational geometry of biomolecular structure, 
    In: Handbook of Computational Statistics, Springer, 2004, 981-1000 (Book chapter).

  9. A.Tropsha, C.W.Carter, S.Cammer, I.I.Vaisman. 
    Simplicial neighborhood analysis of protein packing (SNAPP): a computational geometry approach to studying proteins. 
    Methods Enzymol., 2003, 374, 509-544. [Medline]

  10. M.Masso, I.I.Vaisman. 
    Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach. 
    Biochem. Biophys. Res. Comm., 2003, 305, 2, 322-326 [Medline]

  11. D.Bostick, I.I.Vaisman.  
    A new topological method to measure protein structure similarity. 
    Biochem. Biophys. Res. Comm., 2003, 304, 2, 320-325 [Medline]

  12. O.Shats, I.I.Vaisman, A.Shats, S.Sherman

    13. Sequence-conformation-structure database for amino acid residues in protein structures.
    Bioinformatics,  1999, 15, 6, 525-526. [Medline]

  13. I.I.Vaisman, A.Tropsha, W.Zheng

    14. Compositional Preferences in Quadruplets of Nearest Neighbor Residues in Protein Structures: Statistical Geometry Analysis.
    In: Proceedings of the IEEE Symposia on Intelligence and Systems, 1998, p.163-168.
    [Computer Society Digital Library PDF - subscription required]  [Preprint - PDF]

  14. W.Zheng, S.J.Cho, I.I.Vaisman, A.Tropsha

    15. A New Approach to Protein Fold Recognition Based on Delaunay Tessellation of Protein Structure.
    In: Pacific Symposium on Biocomputing'97, Altman R.B. et al., Eds,
    World Scientific, Singapore, 1997, p.487-496  [Medline]

  15. R.K.Singh, A.Tropsha, I.I.Vaisman

    16. Delaunay Tessellation of Proteins: Four Body Nearest Neighbor Propensities of Amino Acid Residues.
    J. Comput. Biol. 1996, 3, 2, 213-221.  [Medline] [Preprint - PDF]

  16. Vaisman I.I.

    17. Virtual communities at interdisciplinary boundaries
    In: Biocomputing, Hunter L. and Klein T.E., Eds,
    World Scientific, Singapore, 1995, p.756-757.

  17. A.Tropsha, R.K.Singh, I.I.Vaisman and W.Zheng

    18. Statistical geometry analysis of proteins: Implications for inverted structure prediction
    In: Biocomputing, Hunter L. and Klein T.E., Eds,
    World Scientific, Singapore, 1995, p.614-623.  [Medline]

  18. D.Hoffman, S.Laiter, R.K.Singh, I.I.Vaisman, A.Tropsha

    19. Rapid protein structure classification using one-dimensional structure profiles on the BioSCAN parallel computer.
    Comput. Applic. Biosci. 1995, 11, 6, 675-680. [Medline]

  19. S.Laiter, D.Hoffman, R.K.Singh, I.I.Vaisman, A.Tropsha

    20. Pseudotorsional OCCO bacbone angle as a single descriptor of protein secondary structure.
    Protein Science, 1995, 4, 8, 1633-1643. [Medline]

  20. I.I.Vaisman, F.K.Brown, A.Tropsha

    21. Distance Dependence of Water Structure Around Model Solutes.
    J. Phys. Chem., 1994, 98, 21, 5559-5564.

  21. Y.M.Kessler, Y.P.Puhovski, M.G.Kiselev, I.I.Vaisman

    22. Computer simulations of liquid systems: possibilities and principal results.
    In: Chemistry of Non-Aqueous Solutions. Recent Advances, eds. A.I.Popov, G.Mamantov.
    VCH Publishers, New York, 1994, pp.307-373. (Book chapter)

  22. I.I.Vaisman, L.Perera, M.L.Berkowitz

    23. Mobility of stretched water.
    J.Chem.Phys., 1993, 98, 12, 9859-9862

  23. Y.M.Kessler, I.I.Vaisman, M.G.Kiselev, Y.P.Puhovski

    24. Preferential solvation of ions in binary mixed solvents: NMR and simulation data.
    Acta Chim. Hung., 1992, 129, 6, 787-824 (Feature article).

  24. I.I.Vaisman, M.L.Berkowitz

    25. Local structural order and molecular associations in water-DMSO mixtures. Molecular dynamics study.
    J. Am. Chem. Soc., 1992, 114, 20, 7889-7896

  25. Y.P.Puhovski, M.G.Kiselev, I.I.Vaisman, Y.M.Kessler

    26. Structural and dynamic peculiarities of Na+ and Cl- hydration from results of MD experiment.
    In: Thermodynamics of Electrolyte Solutions, ed. G.A.Krestov. Ivanovo, 1992, pp.62-68.

  26. I.I.Vaisman, M.G.Kiselev, Y.P.Puhovski, Y.M.Kessler

    27. The Na+ ion solvation in water- hexamethylphosphorictriamide mixture: Molecular dynamics simulation.
    In: Modelling of Molecular Structures and Properties, ed. J.-L. Rivail ,
    Stud. Phys. Theor. Chem. v.71, Elsevier, Amsterdam, 1990, pp.187-194.

  27. Y.M.Kessler, A.N.Petrov, I.I.Vaisman, V.V.Goncharov, G.A.Alper

    28. The influence of cations on the hydration shell of hexamethylphosphoramide.
    Russ. J. Phys. Chem., 1990, 64, 2, 247-252.

  28. Y.M.Kessler, R.S.Kumeev, I.I.Vaisman, R.B.Lyalina, R.H.Bratishko

    29. Ionic mobilities at infinite dilution: Structural aspects.
    Ber. Bunsenges. Phys. Chem., 1989, 93, 7, 770-782.

  29. M.G.Kiselev, I.I.Vaisman, Y.P.Puhovski, Y.M.Kessler

    30. Thermodynamic properties of the water-HMPT system from molecular dynamics data.
    In: Thermodynamics of Nonelectrolyte Solutions, ed. G.A.Krestov. Ivanovo, 1989, pp.79-84.
    (Chem. Abstr. 112:126600v).

  30. I.I.Vaisman, R.B.Lyalina, Y.M.Kessler, R.S.Kumeev, V.V.Goncharov

    31. Effect of solvent structure on the mobility of ions at infinite dilution.
    Russ. J. Phys. Chem., 1988, 62, 3, 838-840.

  31. M.G.Kiselev, B.G.Abrosimov, I.I.Vaisman, Y.M.Kessler

    32. Error estimation in molecular dynamics experiments with a tabulated intermolecular interaction potential.
    Mol. Simulation, 1988, 1, 5, 321-326.

  32. N.A.Abakumova, I.I.Shamonov, Y.M.Kessler, I.I.Vaisman

    33. Fusibility diagrams of binary systems of water with HMPT, DMF, DEP, DMA, acetone, and THF.
    In: Modern Problems in Physical Chemistry of Solutions. Leningrad, 1981, v.2, pp.47-54.
    (Chem. Abstr. 98:78941a).

  33. 14. Y.M.Kessler, N.A.Abakumova, I.I.Vaisman

    34. The fusion diagrams for the water-dimethylform-amide and water-diethylformamide systems.
    Russ. J. Phys. Chem., 1981, 55, 10, 2682-2684.


Created in July, 1994.  Last update: April, 2006.
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