Mattaparthi Venkata Satish Kumar

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The loops which connect or flank helices/sheets in protein structures are known to be functionally important. However, ironically they also belong to the part of protein whose structure is least accurately predicted. Here, a new method to isolate and analyze loop regions in protein structure is proposed using the spatial coordinates of the solved(More)
Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated (corresponding to neutral pH) poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate(More)
Uracil phosphoribosyltransferase (UPRT) enzyme has immense potential in prodrug-mediated cancer therapy. Molecular docking and enzyme inhibition studies are important for understanding drug–protein interaction in modern drug design. Herein, we experimentally determined the enzyme inhibition constant (K i) of 5-fluorouracil (5FU)—a competitive inhibitor of(More)
Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three(More)
The conformational dynamics of HIV-1 protease (HIV-pr) is known to be essential for ligand binding and determination of cavity size, which changes with several common physiological parameters like temperature, pressure, pH conditions and of course the protein backbone mutations. In this work, the effect of pressure on the conformation and dynamics of HIV-pr(More)
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