Publications (1997-2007)

15. Khandogin J and Brooks CL III*.
Linking folding with aggregation in Alzheimer’s beta-amyloid peptides.
Proc Natl Acad Sci USA 104: 16880-16885. 2007.

 

14. Khandogin J, Raleigh DP, and Brooks CL III*,
Folding intermediate in the villin headpiece domain arises from disruption of an N-terminal hydrogen-bonded network.
J Am Chem Soc 129: 3056-3057, 2007.

 

13. Khandogin J and Brooks CL III*,
Molecular simulations of pH-mediated biological processes.
Annu. Report Comput. Chem., 2007, vol. 3, 3-11, 2007.

 

12. Khandogin J, Chen J, and Brooks CL III*,
Exploring atomistic details of pH-dependent peptide folding.
Proc Natl Acad Sci USA 103: 18546-18550, 2006.

 

11. Khandogin J and Brooks CL III*,
Toward the accurate first-principles prediction of ionization equilibria in proteins.
Biochemistry 45: 9363-9373, 2006.

 

10. Khandogin J* and Brooks CL III,
Constant pH molecular dynamics simulation with proton tautomerism.
Biophys J 89: 141-157, 2005.

 

9. Gregersen BA, Khandogin J, Thiel W, and York DM*,
Smooth solvation method for d-orbital semiempirical calculations of biological reactions II: application to transphosphorylation thio effects in solution.
J Phys Chem B 109: 9810-9817, 2005.

 

8. Khandogin J, Gregersen BA, Thiel W, and York DM*,
Smooth solvation method for d-orbital semiempirical calculations of biological reactions I: implementation.
J Phys Chem B 109: 536-556, 2005.

 

7. Khandogin J and York DM*,
Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods.
Proteins 56: 724-737. 2004.

 

6. Khandogin J, Musier-Forsyth K, and D. M. York*,
Insights into the regioselectivity and RNA binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods.
J Mol Biol 330: 993-1004,2003.

 

5. Khandogin J and York DM*,
Quantum mechanical characterization of nucleic acids in solution: a linear-scaling study of charge fluctuations in DNA and RNA.
J Phys Chem B 106: 7693-7703, 2002.

 

4. Khandogin J, Hu A, and York DM*,
Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization.
J Comput Chem 21: 1562-1571, 2000.

 

3. Khandogin J and Ziegler T*,
A simple relativistic correction to the nuclear spin-spin coupling constant.
J Phys Chem A 104: 113-120. 2000.

 

2. Khandogin J and Ziegler T*,
Density functional study of nuclear magnetic resonance spin-spin coupling constants.
Spectrochim Acta A 55: 607-624, 1999.

 

1. Khandogin Y, Alexeyev AB, Liebermann H-P, Hirsh G, and Buenker RJ*,
Ab initio relativistic CI calculations of the spectroscopic constants and transition probabilities for the low-lying states of the BiOH/HBiO isomers.
J Mol Spectr 186: 22-33,1997.