[gmx-users] apoenzyme wanted

N. S. niyaz.sabir at gmail.com
Wed Sep 24 19:36:19 CEST 2014

Dear Gromacs users,

I study an enzyme (hydrolase), which is known to undergo some
conformational changes upon substrate or inhibitor binding.

Protein Data Bank at rcsb.org has only suitable entries with complex
enzyme-inhibitor structures. I had got might be a stupid idea to make
minimisation and then MD to obtain the apoenzyme conformation. I took out
the ligand from the complex and prepared the protein for MD. I made the
minimisation followed by one nanosecond production MD with Gromacs 4.5.5,
and now I have 9443 protein structures (frames).  I still have a reference,
the main part of the apoenzyme missing a loop of 16 residues.
Theoretically, one could superimpose each of 9443 structures to the
truncated reference apoform one by one, and compare the distances between
several residue C alpha atoms, and choose the best fitted structure among
those 9443. However, you understand I won't do such a job. Could anybody
supply me with a script, or better with a short line of code, to solve the
problem. The problem is to fish out the structure, which is to be close to
the native apoenzyme as much as possible? For now I will not care for the
missing loop position. First I need to catch a golden fish from the pool
populated with another similar 9442 fishes.

Thank you in advance,



Happy journey through the Universe

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