extract putative binding site with sitemap

[Sebastian Contreras]

Hi

I’m trying to do a Little script for extract putative binding sites after execute sitemap. The output of sitemap is a file in mae format that contains the putative “pockets” and the protein. My idea is to load the file in python, do a split for structures and then merge protein with each site and extract residues at 4 angstrom with the Sort module (http://www.schrodinger.com/docs/suite2011general/python_api/api/schrodinger.structutils.sort-module.html ) but i’m a noob programming with python for maestro and I don’t know how to load the module and how can I call the functions (parameters that the functions need is different ) can anyone help me with my problem? Thanks

Best

Sebastian

[Dave Giesen]

Hi Sebastian - thanks for contacting Schrodinger, we're glad that you're giving our Python API a try.

Below is a script that contains some suggestions to get you started.

Dave Giesen

# To import schrodinger modules

from schrodinger import structure

from schrodinger.structutils import analyze

# To cycle through all the structures in a file

for struct in structure.StructureReader('3ligands.mae'):

        print struct.atom_total

# To read the 2nd structure in a file

struct2 = structure.StructureReader('3ligands.mae', index=2).next()

# To merge two structures together (assuming you've already read in

# pocket_structure and protein_structure)

merged_structure = pocket_structure.merge(protein_structure, copy_props=True)

# Find all the atoms from the protein structure within 4 angstroms of the pocket

# structure atoms

pocket_atoms_asl = 'atom.n 1-%d' % pocket_structure.atom_total

asl = 'fillres ((within 4 %s) and not %s)' % (pocket_atoms_asl, pocket_atoms_asl)

nearby_residue_atoms = analyze.evaluate_asl(merged_structure, asl)

# Extract all the nearby atoms into a new structure

nearby_struct = merged_structure.extract(nearby_residue_atoms)

# Write out that structure to a new file

nearby_struct.write('new_file.mae')

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[Sebastian Contreras]

I will try it. Thanks a lot

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