What is Molecular Modeling?

Molecular Modeling, is one of the fastest growing fields in science. It may vary from building and visualizing molecules (click image below for a short animation)...

h2-tag 217K Movie

...to performing complex calculations on molecular systems.

Molecular models fall into four basic categories: skeletal or line; stick, ball-and-stick, and space-fillied or CPK.

wire frame model of ethane
Wire Frame Model -- This model clearly shows the type of atoms in the molecule, the distances between bonds, and angles associated with the atoms. Because the lines drawn are very thin, molecules can very easily be manipulated when viewed on a computer screen.

stick model of ethane
Stick Model -- This model clearly simply shows the whole molecule as a stick as opposed to a wireframe. It is not usually used but can be viewed using Jsmol.

ethane ball and stick model
Ball and Stick Model -- Atoms are represented by balls and bonds are represented as sticks.

ethane space filled model
Space Filled Model (CPK)-- This model shows the space that the molecule will take up. Because of all the points required to draw this molecule on a computer screen you should expect these molecules to be very difficult to manipulate.

Some Basic Aspects of Molecular Modeling

Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical mechanics (Newtonian mechanics) to describe the physical basis behind the models. Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. The interactions between neighbouring atoms are described by spring-like interactions (representing chemical bonds) and Van der Waals forces.

Molecular mechanics (MM) is the simplest and fastest way to evaluate molecular systems. For more details see: Introduction to Molecular Mechanics and Molecular Dynamics


Molecular dynamics (MD) is an important computational tool for understanding the physical basis of the structure, the dynamic evolution of the system, and the function of biological macromolecules.

Below, molecular dynamics simulations are performed on a lipid-protein complex. Shown are the backbone structure of the protein, a bound fatty acid molecule within the protein, and a small shell of water surrounding the protein. The time for the simulation was 100 picoseconds. The graphs give information about the motion of the lipid inside the protein.

dynamics-tag931K Movie

See: Molecular Dynamics Simulations of Adipocyte Lipid-Binding Protein: Effect of Electrostatics and Acyl Chain Unsaturation for more information.

Below a 380 nanosecond Molecular Dynamics Simulation shows the dynamics of water freezing to ice.

See: M. Matsumoto, S. Saito, and I. Ohmine, Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing, Nature 416, 409-413 (2002); http://dx.doi.org/10.1038/416409a for details.


Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site.


crixivan bound to enzyme

Crixivan (molecule - carbon shown in grey-oxygen-red) is a prescription medicine used to treat the symptoms of HIV Infection. Shown is crixivan bound to the protease enzyme active site. See: How do drugs work

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