Sugandhi Rao

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We define geometrical parameters to characterize disulfide bridges using x-ray crystal structure data on small molecules and use them to suggest replacements of amino acids by cysteines in order to introduce disulfide bridges to increase thermal stability in proteins. We also define geometric parameters to identify target amino acids for replacements by(More)
As a part of the development of conformational guidelines for the design of metabolically altered peptidomimetics, we present conformational energy calculations on model dipeptide compounds with glycine (Gly), L-alanine (Ala), alpha-aminoisobutyric acid (Aib), L-tert-butylglycine (Tle), L-phenylglycine (Phg), (alpha, alpha)-diphenylglycine (D phi g),(More)
We present molecular mechanics simulation of the covalent interactions of the potent antitumor antibiotic belonging to the pyrrolo[1,4]benzodiazepine class, anthramycin, with six deoxydecanucleotides, d(GCGCGCGCGC)2, d(G10) X d(C10), d(GCGCGTGCGC) X d(GCGCACGCGC), d(GCGCGAGCGC) X d(GCGCTCGCGC), d(GGGGGAGGGG) X d(CCCCTCCCCC), and d(GGGGGTGGGG) X(More)
Site-directed mutagenesis is a very powerful approach to altering the biological functions of proteins, the structural stability of proteins and the interactions of proteins with other molecules. Several experimental studies in recent years have been directed at estimating the changes in catalytic properties, (rates of binding and catalysis) in(More)
BACKGROUND Quadruple therapy appears to be more effective than standard triple therapy in the management of patients with Helicobacter pylori infection who harbor drug-resistant organisms. No data are available on the relative efficacies of triple and quadruple drug regimens from India. METHODS Consecutive patients with peptic ulcer and H. pylori(More)
We present the results of free energy perturbation/molecular dynamics studies on B-DNA.daunomycin and B-DNA.9-aminoacridine complexes as well as on B-DNA itself in order to calculate the free energy differences between complexes having different base pair sequences. The results generally reproduce the trends observed experimentally, i.e., preferences of(More)
The neighbor-exclusion principle is one of the most general and interesting rules describing intercalative DNA binding by small molecules. It suggests that such binding can only occur at every other base-pair site, reflecting a very large negative cooperativity in the binding process. We have carried out molecular mechanics and molecular dynamics(More)
We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum(More)
In the light of the biological significance of thymine photodimers , studies of the energetics of the dodecanucleotide fragment d( CGCGAATTCGCG )2 have been carried out using the methods of molecular mechanics, with and without incorporation of a thymine dimer in the cis-syn configuration. The results of the calculations suggest that the thymine dimerized(More)