Published papers

  1. V. Lather, V. Kairys and M. X. Fernandes "Quantitative Structure-Activity Relationship Models with Receptor-Dependent Descriptors for Predicting Peroxisome Proliferator-Activated Receptor Activities of Thiazolidinedione and Oxazolidinedione Derivatives", Chemical Biology & Drug Design, 73 (2009) 428-441.

  2. M. D. Altman, A. Akbar, G. S. K. K. Reddy, M. N. L. Nalam, S. G. Anjum, H. Cao, S. Chellappan, V. Kairys, M. X. Fernandes, M. K. Gilson, C. A. Schiffer, T. M. Rana and B. Tidor "HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants", Journal of the American Chemical Society, 130 (2008) 6099-6113.

  3. C. S. Alves, V. Kairys and M. X. Fernandes "Domain motions associated with substrate and inhibitor binding: The relevance of distance matrixes", in Protein Conformation: New Research, L. B. Roswell, editor, Nova Science Publishers (2008), 161-199.

  4. S. Chellappan, V. Kairys, M. X. Fernandes, C. Schiffer, and M. K. Gilson "Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease", PROTEINS: Structure, Function, and Bioinformatics,  68 (2007) 561-567.
    Protiens vol 38 issue 2 cover

  5. V. Kairys and M. X. Fernandes "SitCon: Binding site residue conservation visualization and protein sequence-to-function tool", International Journal of Quantum Chemistry (Special issue: Proceedings from the Sixth European Conference on Computational Chemistry - EUCO-CC6), 107 (2007) 2100–2110.

  6. S. Chellappan, G. S. K. K. Reddy, A. Ali, M. N. L. Nalam, S. G. Anjum, H. Cao, V. Kairys, M. X. Fernandes, M. D. Altman, B. Tidor, T. M. Rana, C. A. Schiffer, and M. K. Gilson "Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis", Chemical Biology & Drug Design, 69 (2007) 298–313.
    CBDD cover

  7. V. Kairys, M. K. Gilson and M. X. Fernandes "Using protein homology models for structure-based studies: Approaches to model refinement", TheScientificWorldJOURNAL, 6 (2006) 1542-1554 (Mini-Review).

  8. V. Kairys, M. X. Fernandes and M. K. Gilson "Screening drug-like compounds by docking to homology models: A systematic study", Journal of Chemical Information and Modeling, 46 (2006) 365-379.

  9. M. X. Fernandes, V. Kairys and M. K. Gilson "Comparing ligand interactions with multiple receptors via serial docking", Journal of Chemical Information and Computer Sciences, 44 (2004) 1961-1970.

  10. V. Kairys, M. K. Gilson and B. Luy "Structural model for an AxxxG-mediated dimer of surfactant-associated protein C", European Journal of Biochemistry, 271 (2004) 2086-2092.

  11. L. Parsons, N. Bonander, E. Eisenstein, M. Gilson, V. Kairys, and J. Orban "Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family", Biochemistry, 42 (2003) 80-89.

  12. V. Kairys and M. K. Gilson "Enhanced docking with the Mining Minima optimizer: Acceleration and side-chain flexibility", Journal of Computational Chemistry, 23 (2002) 1656-1670.

  13. R. M. Minikis, V. Kairys and J. H. Jensen "Accurate intraprotein electrostatics derived from first principles: An effective fragment potential method study of the proton affinities of lysine 55 and tyrosine 20 in turkey ovomucoid third domain", Journal of Physical Chemistry A, 105 (2001) 3829-3837.

  14. M. S. Gordon, M. A. Freitag, P. Bandyopadhyay, J. H. Jensen, V. Kairys, and W. J. Stevens "The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry", Journal of Physical Chemistry A, 105 (2001) 293-305.
    JPCA 2001 cover

  15. V. Kairys and J. H. Jensen "QM/MM boundaries across covalent bonds: A frozen localized molecular orbital-based approach for the effective fragment potential method", Journal of Physical Chemistry A, 104 (2000) 6656-6665.

  16. V. Kairys and J. H. Jensen "Evaluation of the charge penetration energy between the non-orthogonal molecular orbitals using the Spherical Gaussian Overlap approximation", Chemical Physics Letters 315 (1999) 140-144.

  17. V. Kairys and J. D. Head "A quantum chemical cluster study of hydrated halide adsorption on the cathodic Al(111) surface", Surface Science 440 (1999) 169-186.

  18. J. D. Head, V. Kairys, and Y. Shi "Computation of adsorbate vibrational frequencies: methyl, methylidyne and methoxy adsorbed on the Al(111) surface", Journal of Molecular Structure (Theochem) 464 (1999) 153-162.

  19. V. Kairys and J. D. Head "Electric field effects on the geometry and vibrations of charged molecules: the hydroxide ion case", Chemical Physics Letters 288 (1998) 423-428.

  20. V. Kairys and J. D. Head "Geometry optimization of charged molecules in an external electric field applied to F-.H2O and I-.H2O", Journal of Physical Chemistry A 102 (1998) 1365-1370.

  21. V. Kairys and J. D. Head "A theoretical investigation of adsorbate induced surface relaxation effects using cluster models: Al on Si(111)", Surface Science 380 (1997) 283-292.

  22. V. Daujotis and V. Kairys "The mechanism of electroreduction of silver cyanide complexes in aqueous electrolytes-II. Interpretation of SERS data", Electrochimica Acta 42 (1997) 1345-1350.