We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were
We study the role of cations on the stability of double stranded DNA (dsDNA)
molecules.It is known that the two strands of double stranded DNA(dsDNA) have
negative charge due to phosphate group. Cations in the form of salt in the
solution, act as shielding agents thereby reducing the repulsion between these
strands. We study several heterogeneous DNA molecules. We calculate the phase
diagrams for DNA molecules in thermal as well as in force ensembles using
Peyrard-Bishop-Dauxois (PBD) model. The dissociation and the stacking energies
are the two most important factors that play an important role in the DNA
stability. With suitable modifications in the model parameters we investigate
the role of cation concentration on the stability of different heterogeneous
DNA molecules. The objective of this work is to understand how these cations
modify the strength of different pairs or bases along the strand. The phase
diagram for the force ensemble case (a dsDNA is pulled from an end) is compared
with the experimental results
The cations, in form of salt, present in the solution containing DNA play a
crucial role in the opening of two strands of DNA. We use a simple non linear
model and investigate the role of these cations on the mechanical unzipping of
DNA. The Hamiltonian is modified to incoporate the solvent effect and the
cations present in the solution. We calculate the melting temperature as well
as the critical force that is required to unzip the DNA molecule as a function
of salt concentration of the solution. The phase diagrams are found to be in
close agreement with the experimental phase diagrams
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Intracellular positive ions neutralize negative charges on the phosphates of a DNA strand, conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a certain value of salt concentration, the DNA molecule displays an unstable nature in vivo as well as in vitro. We consider a wide range of salt concentrations and study the stability of the DNA double helix using a statistical model. Through numerical calculations, we attempt to explain the different behavior exhibited by DNA molecules in this range. We compare our results with experimental data and find a close agreement.
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