Protein-protein interfaces (PPIs) are an important class of drug targets. We report on the first large-scale validation study on docking into PPIs. DrugScore-adapted AutoDock3 and Glide showed good success rates with a moderate drop-off compared to docking to "classical targets". An analysis of the binding energetics in a PPI allows identifying those interfaces that are amenable for docking. Th...

We present a first-principles study of geometrical structure and energetics of hydrogen adsorbed on hexagonal single-walled silicon nanotubes (SiNTs). The adsorption behaviors of hydrogen molecules in SiNTs are investigated. The binding energies for the most stable physisorbed configurations are calculated to be less than 0.1 eV. The energy barriers are also investigated for dissociation of H2 ...

The kinetics, energetics, and structure of Cyclolinopeptide A binding with Human Serum Albumin were investigated with surface plasmon resonance and circular dichroism. The complex is formed through slow recognition kinetics that is temperature sensitive in the range of 20°C-37°C. The overall reaction was observed to be endothermic (ΔH = 204 kJ mol(-1)) and entropy driven (ΔS = 746 J mol(-1)K(-1...

Using the Kernel Energy Method we apply ab initio quantum mechanics to study the relative importance of weak and strong interactions (including hydrogen bonds) in the crystal structures of the title compounds TDA1 and RangDP52. Perhaps contrary to widespread belief, in these compounds the weak interaction energies, because of their large number and cooperativity, can be significant to the bindi...

Thermodynamic parameters of interactions of calcium-saturated calmodulin (Ca(2+)-CaM) with melittin, C-terminal fragment of melittin, or peptides derived from the CaM binding regions of constitutive (cerebellar) nitric-oxide synthase, cyclic nucleotide phosphodiesterase, calmodulin-dependent protein kinase I, and caldesmon (CaD-A, CaD-A*) have been measured using isothermal titration calorimetr...

Abstract Multidrug and toxic compound extrusion (MATE) transport proteins confer multidrug resistance on pathogenic microorganisms affect pharmacokinetics in mammals. Our understanding of how MATE transporters work, has mostly relied protein structures MD simulations. However, the energetics drug not been studied detail. Many utilise electrochemical H + or Na gradient to drive substrate efflux,...

Invasion of intestinal epithelial cells by Salmonella enterica serovar Typhimurium is an energetically demanding process, involving the transfer of effector proteins from invading bacteria into host cells via a specialized organelle known as the Salmonella pathogenicity island 1 (SPI-1) type 3 secretion system (T3SS). By a mechanism that remains poorly understood, entry of S. Typhimurium into e...

Ligands that bind to the benzodiazepine binding site on the GABA A receptor can attenuate or potentiate cognition. To investigate this property, the chemical determinants favoring selective binding or selective activation of the alpha5beta2gamma2 and alpha1beta2gamma2 GABA A receptor isoforms were examined. A 3D-pharmacophore, developed from a diverse set of BDZR ligands, was used as an initial...