The role played by the degree of folding of protein backbones in explaining the binding energetics of protein-ligand interactions has been studied. We analyzed the protein/peptide interactions in the RNase-S system in which amino acids at two positions of the peptide S have been mutated. The global degree of folding of the protein S correlates in a significant way with the free energy and entha...

Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacem...

in this research, this possibility was investigated the relative stablilty geometry and bindingenergies of the hydrogen bonds of molybdate-phosphonic acid (mpa) complex in gas phase onthe basis of result of ab initio and dft calculations. three dft methods have been applied forcalculations are b3lyp, bp86 and b3pw91 that have been studied in two series of basis sets:d95** and 6-31+g(d,p) for hy...

The Alanine Scanning Energetics database (ASEdb) is a searchable database of single alanine mutations in protein-protein, protein-nucleic acid, and protein-small molecule interactions for which binding affinities have been experimentally determined. In cases where structures are available, it contains surface areas of the mutated side chain and links to the PDB entries. It is useful for studyin...

Background: Development of safe radioprotector is a challenging task. In this study radioprotective effect of sucrose has been demonstrated in calf thymus DNA (CtDNA). Sucrose is a free radical scavenger and also acts as osmolyte and therefore can influence the water activity around DNA and effects of radiation on DNA. Hoechst 33258 was used to probe the possible alteration in physicochemical p...