Wednesday, December 26, 2012

New paper: Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

+Casper Steinmann recently submitted the paper to PLoS ONE and is awaiting announcement on arXiv.org where you can view the manuscript.

This is the first time that a fragment based method has been applied to map out a trajectory of an enzyme - on this case the very popular chorismate mutase.

Abstract
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be 18.3 +/- 3.6$ kcal mol-1 using ONIOM with MP2/cc-pVDZ and EFMO/6-31G(d) for the high and low layers, respectively.

sidenote and totally off topic: you can now reference peoples Google+ profiles directly in blogger in the same way that you do on Google+. Nicely done.

2 comments:

Pedro S said...

I have greatly enjoyed your paper. Could you please add a link to some sample inputs? Will the enhanced Gamess(US) code be distributed by you, or must we wait for that to be included in the next ISU releases?

Casper Steinmann said...

Hi Pedro,

thanks for your interest and very kind comment! I will provide some samples very soon in a blog post with links to input and output. Stay tuned.

You will have to wait for the next ISU release, but my code will be merged very soon. I do, however, have no clue when the next release is due.

Casper