Attractive inter-residue contact energies for proteins have been re-evaluated with the same assumptions and approximations used originally by us in 1985, but with a significantly larger set of protein crystal structures. An additional repulsive packing energy term, operative at higher densities to prevent overpacking, has also been estimated for all 20 amino acids as a function of the number of...

Density functional theory (DFT) calculations were performed to investigate the properties of planar, tubular and conical forms of silicon nanostructures. The evaluated parameters including averaged bond lengths, binding energies, gap energies and dipole moments were then evaluated for the optimized models of study. The results indicated that the bond lengths between silicon atoms are different ...

Density functional theory (DFT) calculations were performed to investigate the properties of planar, tubular and conical forms of silicon nanostructures. The evaluated parameters including averaged bond lengths, binding energies, gap energies and dipole moments were then evaluated for the optimized models of study. The results indicated that the bond lengths between silicon atoms are different ...

The density functional theory (DFT) calculations were used to get information concerning the interaction of curcumin with pristine and N-doped TiO2 anatase nanoparticles. Three adsorption geometries of curcumin over the TiO2 anatase nanoparticles were studied in order to fully exploit the sensing properties of TiO2 nanoparticles. Curcumin molecule adsorbs on the fivefold coordinated titanium si...

Cosmic high energy neutrinos are inextricably linked to the origin of cosmic rays which is one of the major unresolved questions in astrophysics. In particular, the highest energy cosmic rays observed possess macroscopic energies and their origin is likely to be associated with the most energetic processes in the Universe. Their existence triggered a flurry of theoretical explanations ranging f...

The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG...

Pairwise contact energies for 20 types of residues are estimated self-consistently from the actual observed frequencies of contacts with regression coefficients that are obtained by comparing "input" and predicted values with the Bethe approximation for the equilibrium mixtures of residues interacting. This is premised on the fact that correlations between the "input" and the predicted values a...

We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RE...