Theoretical chemists have always strived to perform quantum mechanics (QM) calculations
on larger and larger molecules and molecular systems, as well as condensed phase …

The absorption properties of chromophores in biomolecular systems are subject to several
fine‐tuning mechanisms. Specific interactions with the surrounding protein environment …

Semi-empirical (SE) methods are derived from Hartree–Fock (HF) or Density Functional
Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are …

Drug resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease (PR) was
found in clinical treatment of HIV patients with the drug amprenavir (APV). In order to …

At present, the calculated binding free energy obtained using the molecular
mechanics/Poisson-Boltzmann (Generalized-Born) surface area (MM/PB (GB) SA) method is …

A new version of systematic molecular fragmentation is presented which provides a
hierarchy of estimates for the energy, and other properties, of large molecules with a …

Avidin− biotin is one of the strongest protein− ligand binding systems, with broad
applications in biomedical science. Here we report a quantum-based computational study to …

Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to
investigate the effect of polarization on the binding of ligands to human α-thrombin based on …

Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2
protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with …

We report direct folding of a 17-residue helix protein (pdb: 2I9M) by standard molecular
dynamics simulation (single trajectory) at room temperature with implicit solvent. Starting …