The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

An overview is provided of the capabilities for the current versions of the BOSS and MCPRO
programs for molecular modeling of organic and biomolecular systems. Recent applications …

Quantitative free energy computation involves both using a model that is sufficiently faithful
to the experimental system under study (accuracy) and establishing statistically meaningful …

The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …

We present a method for conformational search of complex molecular systems such as
macrocycles and protein loops. The method is based on perturbing an existing conformation …

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal
antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is …

Incorporation of effective backbone sampling into protein simulation and design is an
important step in increasing the accuracy of computational protein modeling. Recent …

We consider the problem of loop closure, ie, of finding the ensemble of possible backbone
structures of a chain segment of a protein molecule that is geometrically consistent with …

To accurately predict protein conformations in atomic detail, a computational method must
be capable of sampling models sufficiently close to the native structure. All-atom sampling is …

Many limitations of current computer-aided drug design arise from the difficulty of reliably
predicting the binding affinity of a small molecule to a biological target. There is thus a strong …