Download Replicate OPM - MultiscaleLab

Project MSI 1 – Deadline 30th April at 23.59
Create a python module which given a PDB from the protein data bank returns a
HTMD molecule which contains the PDB plus one or two slabs of dummy atoms
representing the position of the membrane leaflet (similarly to OPM
http://opm.phar.umich.edu/). Write a short report describing the algorithm
used and the results compared to a set of 5 proteins taken from the OPM
(http://opm.phar.umich.edu/about.php?subject=other)
TIPS
1) Start by writing a function that creates a molecule with a slab of dummy
atoms.
def dummy_leaflet(pmin, pmax, z, spacing=3.0):
…
where pmin is the lower left corner of the slab in the xy plane and pmax is the
upper right corner, spacing is the distance between dummy atoms. All dummy
atoms have the same z. The function returns a Molecule object. Inside the
function use
mem = Molecule()
mem.empty(Ni*Nj)
to create an empty molecule with Ni*Nj atoms and then set manually the
attributes record, beta, resid, resname, name, coords for each dummy atom in
the slab. Take a dummy slab from OPM as example.
2) Aromatic residues form anchors on the membrane, use the orientation of their
ring plane to orient the protein (the membrane is placed in xy plane). The
function mol.rotateBy(rotationMatrix([1,0,0],radiants)) helps in rotating the
protein around the x axis by radiants for example
3) use the position of hydrophic and basic+acidic atoms to place the membrane
leaflet at the right z position compared to the reoriented protein.
4) improve on the above algorithm