The picture above shows the catalytic triade of a Plasmodium Falciparum serine protease together with a functional group description generated by DYN-MAP (PyMol plug-in). In fact, my Ph.D project has as main subjects molecular modeling and protein-protein docking for drug discovery. I want to design inhibitors based on the known scaffold of the cyclotides to inhibit specifically two subtilisin-like serine proteases (PfSUB1, PfSUB2). There is no structural data on these two proteins, therefore it is very important to generate a reliable model to work with. The inhibitors will then be tested experimentally with tests on the enzyme, if available, or on the parasite.

DYN-MAP is a python-based program that generates maps of functional groups present in a protein and visualize them using dynamic parameters. To each aminoacid is assigned a set of functional groups based on its chemical properties. The functional groups (hydrogen acceptor, donor, hydrophobic, charged and aromatic) are displayed by spheres of variable radius. The radius value depends on two "dynamic parameters": surfscore, rmsf.

The picture below it is a sample result of DYNMAP. DYNMAP is also present in thePyMol wikipedia page.

Why DYNMAP could be useful:

1. Visualize distribution of functional groups in a protein, their solvent accessibility and their spatial fluctuation.
2. Compare functional groups (dynmaps) among homologous proteins or mutants.
3. Run automatically GROMACS molecular dynamics.

Click here to download DYNMAP ver.1.0 2007

Requirements:

Biopython 1.43, CheetahTemplate 2.0, Python 2.4, PyMol 0.99, GROMACS 3.3.1, MSMS

not availabe yet