Publications
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1999. Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion. J. Chem. Phys.. 111:1407–1414.
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1998. Accurate DNA dynamics without accurate long range electrostatics. J. Am. Chem. Soc.. 120:10928–10937.
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1998. DNA crossovers and type II DNA topoisomerases: A thermodynamical study. J. Mol. Biol.. 284:1279–1287.
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1998. Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method. J. Chem. Phys.. 109:1567–1574.
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1998. Folding and Aggregation of Designed Protein Chains. Proc. Natl. Acad. Sci. Usa. 95:12930–1293.
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1998. Hydration and recognition of methylated CpG steps in DNA. Embo J.. 17:2709–2718.
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1998. Hierarchy of fast motions in protein dynamics. J. Phys. Chem. B. 102:473–479.
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1998. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J.. 74:72–81.
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1998. A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove. J. Biomol. Struct. Dyn.. 16:535–46.
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1998. Symmetry and chirality in topoisomerase II-DNA crossover recognition. J. Mol. Biol.. 284:1289–1299.
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1998. A soft, mean–field potential derived from crystal contacts for predicting protein–protein interactions. J. Mol. Biol.. 283:1037–1047.
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1997. Collective-variable Monte Carlo simulation of DNA. J. Comp. Chem.. 18:2001–2011.
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1997. Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of St\H ormer-leapfrog integrators. J. Comput. Phys.. 136:354–365.
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1997. A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain .1. Formulation and test on a hexadecapeptide. J. Chem. Phys.. 106:5260–5270.
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1997. Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: An internal coordinate molecular modeling study. J. Biomol. Struct. Dyn.. 14:703–714.
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1997. Effect of cytosine methylation on DNA-DNA recognition at CpG steps. J. Mol. Biol.. 270:328–335.
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1997. Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method. J. Chem. Phys.. 107:1941–1947.
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1997. Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers. J. Comput. Chem.. 18:1354–1364.
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1996. Cruciform structures and functions. Q. Rev. Biophys.. 29:279–307.
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1996. Finding and visualizing nucleic acid base stacking. J Mol Graph. 14:6–11.
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1996. Molecular modelling study of the netropsin complexation with a nucleic acid triple helix. J. Biomol. Struct. Dyn.. 14:293–302.
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1995. Efficient conformational space sampling for nucleosides using internal coordinate Monte-Carlo simulations and a modified furanose description. J. Comput. Chem.. 16:667–680.
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1995. Estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes. Biophys. J.. 69:840–848.
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1995. Investigation of the conformational properties of a {$\beta$}-(1-3) branched {$\beta$}-(1-6) heptasacchardie elicitor and its analogues by internal coordinate stochastic dynamics. Carbohydr. Res.. 279:41–57.
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1995. LONG TIMESTEP DYNAMICS OF PEPTIDES BY THE DYNAMICS DRIVER APPROACH. Proteins-structure Function and Genetics. 21:282–302.