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Takes a set of task operations from the user in order to more precisely specify a set of residues to analyze via ddG scanning. Individually mutates each of the residues to alanine (or whatever other residue is defined in the task operations) and calculates the change in binding energy (ddG).
<DdGScan name="(& string)" task_operations="(comma-delimited list of task operations)" repeats="(1 &Size)" scorefxn="(&scorefxn)" report_diffs="(1 &bool)" write2pdb="(0 &bool)" />
Sample query to obtain results from database:
SELECT
structures.tag AS tag,
residues.name3 AS wt,
residue_pdb_identification.residue_number as rosetta_resNum,
residue_pdb_identification.pdb_residue_number AS pdb_resNum,
residue_pdb_identification.chain_id AS chain,
ddg.mutated_to_name3 AS mut,
ddg.ddG_value,
batches.description
FROM ddg
INNER JOIN structures ON structures.struct_id=ddg.struct_id
INNER JOIN residue_pdb_identification ON
residue_pdb_identification.struct_id=structures.struct_id
AND residue_pdb_identification.residue_number=ddg.resNum
INNER JOIN residues ON residues.struct_id=structures.struct_id
AND residues.resNum=ddg.resNum
INNER JOIN batches ON batches.batch_id=structures.batch_id;