• B Jayaram

      Articles written in Journal of Chemical Sciences

    • DNA minor groove binding of small molecules: Experimental and computational evidence

      Prateek Pandya Md Maidul Islam G Suresh Kumar B Jayaram Surat Kumar

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      Eight indole derivatives were studied for their DNA binding ability using fluorescence quenching and molecular docking methods. These indole compounds have structural moieties similar as in few indole alkaloids. Experimental and theoretical studies have suggested that indole derivatives bind in the minor groove of DNA. Thermodynamic profiles of DNA complexes of indole derivatives were obtained from computational methods. The complexes were largely stabilized by H-bonding and van der Waal’s forces with positive entropy values. Indole derivatives were found to possess some Purine (Pu) - Pyrimidine (Py) specificity with DNA sequences. The results obtained from experimental and computational methods showed good agreement with each other, supported by their correlation constant values.

    • Bhageerath—Targeting the near impossible: Pushing the frontiers of atomic models for protein tertiary structure prediction

      B Jayaram Priyanka Dhingra Bharat Lakhani Shashank Shekhar

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      Protein folding, considered to be the holy grail of molecular biology, remains intractable even after six decades since the report of the first crystal structure. Over 70,000 X-ray and NMR structures are now available in protein structural repositories and no physico-chemical solution is in sight. Molecular simulation methodologies have evolved to a stage to provide a computational solution to the tertiary structures of small proteins. Knowledge base driven methodologies are maturing in predicting the tertiary structures of query sequences which share high similarities with sequences of known structures in the databases. The void region thus seems to be medium (> 100 amino acid residues) to large proteins with no sequence homologs in the databases and hence which has become a fertile ground for the genesis of hybrid models which exploit local similarities together with ab initio models to arrive at reasonable predictions.We describe here the development of Bhageerath an ab initio model and Bhageerath-H a hybrid model and present a critique on the current status of prediction of protein tertiary structures.

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