* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Replicate OPM - MultiscaleLab
Structural alignment wikipedia , lookup
Protein design wikipedia , lookup
Bimolecular fluorescence complementation wikipedia , lookup
Protein structure prediction wikipedia , lookup
Protein domain wikipedia , lookup
Protein folding wikipedia , lookup
Protein mass spectrometry wikipedia , lookup
Homology modeling wikipedia , lookup
Implicit solvation wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Protein purification wikipedia , lookup
Protein moonlighting wikipedia , lookup
Circular dichroism wikipedia , lookup
Trimeric autotransporter adhesin wikipedia , lookup
List of types of proteins wikipedia , lookup
Western blot wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
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