A new computational method for deducing quantitative structure-activity relationships (QSARs) using structural data from ligand-macromolecule complexes is presented. First, the ligand-macromolecule interaction energy is computed for a set of ligands using molecular mechanics calculations. Then, by selecting and scaling components of the ligand-macromolecule interaction energy that show good pre...

a thermodynamic study of copper ions by jack bean urease (jbu) was carried out at two temperatures of 27 and 37?c in tris buffer (30 mm; ph=7.0) using an isothermal titration calorimetry. there is a set of twelve identical and non-interacting binding sites for copper ions. the intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 285 µm and ?15.2 kj/mol at 27?c and 3...

by employing the theoretical method based on tight-binding, we study electronic band structure of single-wall carbon nanotube (cnt) superlattices, which the system is the made of the junction between the zigzag and armchair carbon nanotubes. exactly at the place of connection, it is appeared the pentagon–heptagon pairs as topological defect in carbon hexagonal network. the calculations are base...

Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom...

A tight-binding total-energy (TBTE) method has been developed to interpolate between firstprinciples results describing the dissociation of molecules at surfaces. The TBTE scheme requires only a relatively small number of ab initio energies as input and gives a reliable global representation of the ab initio potential energy surface to within 0.1 eV accuracy compared to the ab initio results. T...

In solution, the TATA box binding protein from S. cerevisiae (yTBP) is only minimally oriented when bound to the adenovirus major late promoter (AdMLP) and the yeast CYC1 promoter. At equilibrium, approximately 60% of the complexes are assembled in the orientation observed within crystal structures; 40% are assembled in the opposite orientation. Here we use stopped-flow fluorescence resonance e...

a novel ternary schiff base ligand (hl) of ono type and its copper (ii) complex weresynthesised using 2-aminophenol and o-acetoacetotoluidide. they have been characterised by theusual analytical and spectral methods. the interaction of the complex with calf-thymus (ct)dna has been investigated by uv-vis, viscosity measurement, cyclic voltammetry anddifferential pulse voltammetry studies. the re...

The potential energy surfaces of the neutral and anionic thymine-water complexes are investigated using high-level ab initio calculations. Both dipole-bound (DB) and valence-bound (VB) anionic forms are considered. Four minima and three first-order stationary points are located, and binding energies are computed. All minima, for both anions, are found to be vertically and adiabatically stable. ...

Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/AIDS) is a disease pertained to the human immune system. Given its crucial role in viral replication, HIV-1 protease (HIV-1 PR) is a prime therapeutic target in AIDS therapy. In this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in HIV-1 PR in...

Hydrogen storage capacity of Si-coated B80 fullerene was investigated based on density functional theory calculations within local density approximation and generalized gradient approximation. It is found that Si atom prefer to be attached above the center of pentagon with a binding energy of -5.78 eV. It is inferred that this binding is due to the charge transfer between the Si atom and B80 ca...