Afreen Nizar

BID - 19001

BID – 604 Molecular Modeling Principles and Techniques

Assignment - I
Applications of Molecular mechanics

Molecular Mechanics is a computational method that computes the potential

energy surface for a particular arrangement of atoms using potential functions
that are derived using classical physics. These equations are known as a force-
field.

 Obtaining a reasonably good geometry (in structures where pi electrons

are not involved.
 As a starting point for further calculations, such as semi-empirical, ab
initio, or density functional.
 Searching the potential energy surface for minimum energy
conformations.
 Molecular model was developed out of a need to describe molecular
structures and properties in as practical a manner as possible. The great
computational speed of molecular mechanics allows for its use in
procedures such as molecular dynamics, conformational energy
searching, and docking. All the procedures require large numbers of
Energy evaluations.
 Molecular mechanics potential energy functions have been used to
calculate binding constant protein folding kinetics, protonation equilibria,
active site coordinates and to design binding sites.