Petras Kundrotas

1. Kundrotas, P.J. and Alexov, E. “Predicting interacting and interfacial residues using continuous sequence segments” Int. J. Biological Macromolecules (accepted).

2. Brook, K., Talley, K., Coley, K., Kundrotas P.J. and Alexov, E. “Optimization of electrostatic interactions in protein-protein complexes”  Biophys. J. (accepted)

3. Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. “Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families ” J. Bioinformatics Comput Biol.(2007) 5:693-715 pdf

4. Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. “BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families ” Int. J. Biological Macromolecules (2007) 41, 114-119. pdf

5. Kundrotas, P.J. and Alexov, E. “Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives” BMC Bioinformatics (2006) 7:503. pdf

6. Kundrotas, P.J. and Alexov, E.. “PROTCOM: searchable database of protein complexes enhanced with domain-domain structures” Nucleic Acids Research (2007), 35, D575-D579. pdf.

7. Kundrotas, P.J. and Alexov, E.. “Predicting 3D  structures of transient protein-protein complexes by homology” BBA (2006) 1764, 1498-1511 pdf...

8. Kundrotas, P.J. and Alexov, E.. “Electrostatic properties of protein-protein complexes” Biophys. J. (2006), 91, 1724-1736. pdf.

9. P. J. Kundrotas, Statistical properties of flexible polypeptide chains, Biomacromolecules .6, 3010 (2005). pdf

10. P.J. Kundrotas, Monte Carlo Method: Some of its application to problems in protein science. In “Modern Methods for Theoretical Physical Chemistry of Biopolymers”, ed. by E.B.Starikow, S. Tanaka and J. P. Lewis, Elsevier, (2006) Chapter 15, pp. 276– 306. link

11. P. J. Kundrotas and A. Karshikoff, Charge sequence coding in statistical models of unfolded proteins, Biochimica et Biophysica Acta, 1702, 1 (2004).pdf

12. P. J. Kundrotas and A. Karshikoff, Electrostatic interactions in unfolded proteins: Implication for protein stability [Review], Current Topics in Peptide & Protein Research, 6, 21 (2004).

13. P. J. Kundrotas and A. Karshikoff, Effects of charge-charge interactions on dimensions of unfolded polypeptide chains: Monte Carlo studies, J. Chem. Phys.,119, 3574 (2003) (Also selected for August 1, 2003 issue of the Virtual Journal of Biological Physics Research). pdf

14. P. J. Kundrotas and A. Karshikoff, A model for calculation of electrostatic interactions in unfolded proteins, Phys. Rev. E, 65, 011901 (2002).pdf

15. P. J. Kundrotas and A. Karshikoff, Modelling of denatured state for calculation of electrostatic contribution to protein stability, Protein Science, 11, 1681 (2002). pdf

16. R. Häggkvist, A. Rosengren, D. Andren, P. J. Kundrotas, P.-H. Lundow, and K. Markström, A Monte Carlo sampling scheme for the Ising model, J. Stat. Phys., 114, 455 (2004).

17. R. Häggkvist, A. Rosengren, D. Andren, P. J. Kundrotas, P.-H. Lundow, and K. Markström, Computation of the Ising partition function for 2-dimensional square grids, Phys. Rev. E, 69, 046104 (2004).

18. S. A. Basylko, P. J. Kundrotas, V. A. Onischouk, E. E. Tornau, and A. Rosengren, Coulomb gap in a model with finite charge transfer energy, Phys. Rev. B, 63, 024201 (2001).

19. P. J. Kundrotas, V. A. Onischouk, and A. Rosengren, Coulomb correlation gap: Finite-size analysis, Phys. Lett. A, 287, 278 (2001).

20. J. Banys, P. J. Kundrotas, C. Klimm, A. Klöpperpieper, and G. Völkel, Phase diagram of the mixed crystals betaine phosphate – betaine phosphite. Comparison of experimental and Monte Carlo studies, Phys. Rev. B, 61, 3159 (2000).

21. S. A. Basylko, V. A. Onischouk, P. J. Kundrotas, E. E. Tornau, and A. Rosengren, Ground-state study of a  donor-acceptor model with finite charge-transfer energy, Phys. Lett. A, 271, 134 (2000).

22. P. J. Kundrotas, J. Banys, C. Klimm, G. V  "olkel, and A. Rosengren, Dielectric measurements and Monte Carlo studies of mixed crystals (betaine phosphate)_x(betaine phosphite)_1-x at small x, Lithuanian J. Physics, 38, 184 (1998).

23. P. J. Kundrotas, S. Lapinskas, and A. Rosengren, Theoretical study of the oxygen-induced missing-row reconstruction on the Rh(110) surface, Surface Science, 377-379, 7 (1997).

24. P. J. Kundrotas, S. Lapinskas, and A. Rosengren, A model of adsorbate-induced missing-row reconstructions of the (110) surface of fcc metals, Phys. Rev. B 56, 6486 (1997).

25. E. E. Tornau, P. J. Kundrotas, and A. Rosengren, Effect of oxygen ordering and copper substitutions on superconducting  temperature and hole amount of Y-Ba-Cu-O compounds, Lithuanian J. Physics, 37, 73 (1997).

26. G. Grigelionis, P. J. Kundrotas, E. E. Tornau, and A. Rosengren, Modelling of Y and Cu substitution in YBa₂Cu₃O_6+x: effect on oxygen ordering and superconducting temperature, Supercond. Sci. Technol 9, 927 (1996).

27. P. J. Kundrotas, E. E. Tornau, and A. Rosengren, Dynamics of oxygen ordering in the cell-doubled phase of YBa₂Cu₃O_6+x, Phys. Rev. B, 54, 4357 (1996).

28. E. E. Tornau, P. J. Kundrotas, and A. Rosengren, Holes amount and aging of quenched samples of YBa₂Cu₃O_6+x, Physica C, 269, 198 (1996).

29. P. J. Kundrotas, E. E. Tornau, and A. Rosengren, Non-chain superstructures in YBa₂Cu₃O_6.375 at finite temperatures, J. Phys. Cond. Matt., 7, 7253 (1995).

30. P. J. Kundrotas, S. Lapinskas, and A. Rosengren, Phase transitions in the three-state antiferromagnetic Potts model, Phys. Rev. B, 52, 9166 (1995).

31. E. E. Tornau, P. J. Kundrotas, S. Lapinskas, and A. Rosengren, Why does Y₂Ba₄Cu₇O_14+x not exhibit a plateau in its Tc(x) dependence? Prediction from oxygen ordering, Solid State Comm., 91, 393 (1994).

32. E. E. Tornau, P. J. Kundrotas, S. Lapinskas, and A. Rosengren Comparison of oxygen ordering and charge transfer in YBa₂Cu₃O_6+x and Y₂Ba₄Cu₇O_14+x compounds, Physica C, 235-240, 869 (1994).

33. V. E. Zubkus, P. J. Kundrotas, and A. S. Orliukas, Monte Carlo study of oxygen ordering processes in YBa₂Cu₃O_7-x, J. Phys. Condens. Matt., 4, 83 (1992).

34. V. E. Zubkus, G. M. Vujicic, P. J. Kundrotas, and V. V. Tatarskij, Oxygen ordering and states of holes in YBa₂Cu₃O_6+x, Phys. Rev. B, 45, 10728 (1992).

35. V. E. Zubkus, O. E. Parfionov, E. E. Tornau, and P. J. Kundrotas, Asymmetry of phase diagram and influence of oxygen ordering on holes pairing in YBa₂Cu₃O_6+x, Physica C, 198, 141 (1992).

36. V. E. Zubkus, E. E. Tornau, S. Lapinskas, and P. J. Kundrotas, Phase diagrams of oxygen ordering in high-temperature superconductors RBa₂Cu₃O_7-x, Phys. Rev. B, 43, 13112 (1991).

37. V. E. Zubkus, P. J. Kundrotas, S. N. Molotkov, V. V. Tatarskij, and E. E. Tornau, Monte Carlo study of surface reconstruction in Ge(001), Surface Science, 243, 295 (1991).

38. V. E. Zubkus, P. J. Kundrotas, S. Lapinskas, and V. N. Kashcheev, Diffusion in crystals with competing interactions of migrating ions, Physica Status Sol. (b), 158 , 51 (1990).

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For contact information, please, see Alexov webpage  at Clemson University

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