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A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free(More)
We apply continuum solvent models to investigate the relative stability of various conformational forms for two RNA sequences, GGAC(UUCG)GUCC and GGUG(UGAA)CACC. In the first part, we compare alternate hairpin conformations to explore the reliability of these models to discriminate between different local conformations. A second part looks at the(More)
Discretization is used in click-based graphical passwords so that approximately correct entries can be accepted by the system. We show that the existing discretization scheme of Birget et al.(2006) allows for false accepts and false rejects because the tolerance region is not guaranteed to be centered on the original click-point, causing usability and(More)
Molecular dynamics simulation in explicit solvent and continuum solvent models are applied to investigate the relative stability of A- and B-form helices for two DNA sequences, dA10-dT10 and dG10-dC10 in three structural forms. One structural form is based on an unrestrained molecular dynamics (MD) trajectory starting from a canonical B-DNA structure, the(More)
We have presented a detailed analysis for structure determinations for the DNA duplex d(CGCAAAAATGCG) obtained from X-ray crystallography, nuclear magnetic resonance, and molecular dynamics simulation. Each of the structures for the duplex deviates from the structure of the canonical form of B-DNA in a number of observable characteristics. Specifically, the(More)
The substrate sequence specificity of the cdc2 protein kinase from Pisaster ochraceus has been evaluated. The peptide, Ac-Ser-Pro-Gly-Arg-Arg-Arg-Arg-Lys-amide, serves as an efficient cdc2 kinase substrate with a Km of 1.50 +/- 0.04 microM and a Vmax. of 12.00 +/- 0.18 mumol/min per mg. The amino acid sequence of this peptide is not based on any sequence in(More)
Comparisons of experimental and calculated interproton nuclear Overhauser effect (NOE) buildup curves for duplex d(CGCGAATTCGCG)2 have been made. The calculated NOEs are based on molecular dynamics simulations including counterions and water and on the single-structure canonical A, B, and crystal forms. The calculated NOE effects include consideration of(More)
The nucleotide sequence for human myelin-associated glycoprotein (MAG) and its deduced amino acid sequence, obtained by analysis of two overlapping cDNA clones isolated from a human brain cDNA library, is presented and compared to that reported for rat MAG. The sequence provides an open reading frame of 1,878 nucleotides encoding a peptide of 626 amino(More)
Discretization is used in click-based graphical passwords so that approximately correct entries can be accepted by the system. We show that the existing discretization scheme of Birget et al.(2006) allows for false accepts and false rejects because the tolerance region is not guaranteed to be centered on the original click-point, causing usability and(More)