Animations

• Tetrahedral Intermediate Formation in Trypsin
• Protein Visualization using pyMol
• Undressing a Zeolite using pyMol
• Folding of a Five-Helix Protein
• Trypsin-Benzamidine complex reproduced

 

Tetrahedral Intermediate Formation in Trypsin

MD/FEP/EVB snapshots from 100 ps around the transition state in the formation of the tetrahedral intermediate in trypsin.

You can read more about this calculation HERE

Protein Visualization using pyMol

This animation demonstrates some of the most common ways of visualize proteiens using pyMol.

You can learn more about the techniques used in this video in the pyMol resouces.

Undressing a Zeolite using pyMol

This animation demonstrates some ways of visualize molecular structures using pyMol.

You can learn more about the techniques used in this video in the pyMol resouces.

Folding of a Five-Helix Protein

This nice video made by the Theoretical and Computational Biophysics Group from the NIH Center for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) demonstrates the potential of computational chemistry in finding native protein structures.

Related paper:

Structural characterization of λ -repressor folding from all-atom molecular dynamics simulations.
Yanxin Liu, Johan Strümpfer, Peter L Freddolino, Martin Gruebele, and Klaus Schulten.
Journal of Physical Chemistry Letters, 3:1117-1123, 2012

Trypsin-Benzamidine complex reproduced

MD simuation that reproduces the crystallographic trypsin-benzamidine complex. Read more about this simulation HERE.