Publications of Surjit B. Dixit

(Email me if you want a reprint of any article in this list)

1)      S.B. Dixit and D.L. Beveridge, “ABCD: A novel RDBMS and related web based tools for the analysis of sequence directed structural properties of DNA”,  Bioinformatics 2006 Apr 15;22(8):1007-9.

2)      S.B. Dixit, S.Y. Ponomarev and D.L. Beverdige, “Root mean square deviation probability analysis of molecular dynamics trajectories of DNA”, Accepted in J Chem Inf Mod

3)      D.L. Beveridge, S.B. Dixit, B.L. Kormos, B. Jayaram and A. Baranger, “Recent progress in molecular dynamics simulations on protein-nucleic acid complexes”, in Computational Studies of DNA and RNA (2005) Ed. J. Sponer and F. Lankas. Springer Verlag (In press)

4)      C. Chipot, X. Rozanska and S.B. Dixit, “Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein”. J Comput Aided Mol Des 2005 Nov;19(11):765-70.

5)      S.B. Dixit, D.L. Beveridge et al. “Molecular dynamics simulations of the 136 unique tetra nucleotide sequences of DNA oligonulceotides. 2. Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps”, Biophys J 2005 Dec;89(6):3721-40.

6)      S.B. Dixit, D.Q. Andrews and D.L. Beveridge, “Induced fit and entropy of structural adaptation in the complexation of CAP and l repressor with cognate DNA sequences”. Biophys J 2005 May;88(5):3147-57.

7)      S.B. Dixit and D.L. Beveridge, “Axis curvature and ligand induced bending in the CAP-DNA oligomers”. Biophys J 2005 Jan;88(1):L04-6.

8)      S.B. Dixit, F. Petici and D.L. Beveridge, “Structure and axis curvature in two dA6.dT6 DNA oligonucleotides: Comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy”. Biopolymers 2004 Dec 15;75(6):468-79.

9)      D.L. Beveridge, D.A. Case, T.E. Cheatham, S.B. Dixit et al. “Molecular dynamics simulations of the 136 unique tetra nucleotide sequences of DNA oligonulceotides. 1. Research Design, informatics, and results on d (CpG) steps”, Biophys J 2004 Dec;87(6):3799-813.

10)   D.L. Beveridge, S.B. Dixit et al. “Molecular dynamics simulations on DNA and protein-DNA complexes: recent progress on sequence effects, conformational stability, axis bending structural bioinformatics”, in Nucleic Acids: Curvature and Deformation. Recent Advances and New Paradigms. Ed. N. Stellwagen and U. Mohanty, ACS (DC), 2004, 13-64.

11)   D.L. Beveridge, S.B. Dixit, G. Barreiro and K.M. Thayer, “Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting”, Biopolymers, 2004, 73, 380-403.Biopolymers 2004 Feb 15;73(3):380-403.

12)   M. Bhandarkar, R. Brunner, C. Chipot, A. Dalke, S.B. Dixit, J. Phillips et al. NAMD Version 2.5, 2003, Theoretical Biophysics Group, Beckman Institute, University of Illinois. http://www.ks.uiuc.edu/Research/namd/current/ug/

13)   B. Jayaram, K.J. McConnell, S.B. Dixit and D.L. Beveridge, “Free energy component analysis of 40 protein-DNA complexes: A consensus view of the thermodynamics of binding at the molecular level”, J Comput Chem 2002 Jan 15;23(1):1-14.

14)   S.B. Dixit and C. Chipot, “Can absolute free energies of association be estimated from molecular simulation? The biotin-streptavidin system revisited”, J Phys Chem A, 2001, 107, 9795-9.

15)   P. Kalra, A. Das, S.B. Dixit and B. Jayaram, “Free energy analysis of enzyme-inhibitor binding: The carboxypeptidase A-inhibitor complexes”, Ind J Chem, 2000, 39A, 262-73.

16)   S.B. Dixit, N. Arora and B. Jayaram, “How do Hydrogen bonds contribute to protein-DNA recognition”, Proceedings of the X1 Conversation on Biomolecular Sterodynamics, Eds. R .H. Sharma and M .H. Sharma, Adenine Press (NY), 2000, 109-12.

17)   B. Jayaram, K.J. McConnell, S.B. Dixit ad D.L. Beveridge. “Free energy analysis of protein-DNA binding: The EcoRI-endonuclease-DNA complex”, J Comput Phys, 1999, 151, 333-357.

18)   S.B. Dixit and B. Jayaram, “Role of hydrogen bonds in protein-DNA recognition: A comparison of generalized Born and finite difference Poisson-Boltzmann solvation treatments”, J Biomol Struct Dyn 1998 Oct;16(2):237-42.

19)   S.B. Dixit, R. Bhasin, E. Rajashekaran and B. Jayaram, “Solvation thermodynamics of amino acids: Assessment of electrostatic contribution and force field dependence”, J Chem Soc Faraday Trans, 1997, 93, 1105-13.