Table 1 Summary of ‘.pdb’ files used. Each ‘.pdb’ file with its corresponding nickname that we use in subsequent sections is listed in the table, along with a brief description of the protein and/or ligand the file contains
Ligand/Protein/Complex Nickname | ‘.pdb’ File | Details |
|---|---|---|
Protein | protein.pdb | ABC transporter SBP (4WT7) which is downloaded from the PDB as a dimer |
Allitol | allitol.pdb | Allitol (X9X) which is isolated from protein.pdb |
Sorbitol | sorbitol.pdb | Sorbitol (SOR) which is generated via conversion through OpenBabel and ‘molfile2params’ code |
Old Protein | proall.pdb | Protein-allitol complex which is the protein.pdb file but modified to be a monomer |
New Protein | prosor.pdb | Protein-sorbitol complex which is essentially proall.pdb plus sorbitol.pdb minus allitol.pdb; the sorbitol molecule is docked in the binding pocket of the protein aligned to the carbon backbone of the allitol molecule before deleting allitol |
New Protein after MinMover | minprosor.pdb | Protein-sorbitol complex after being run through the MinMover code |
Mutated Protein | finprosor.pdb | Protein-sorbitol complex with selective mutation of 5 residues |
New Protein after FastRelax | fastprosor.pdb | Protein-sorbitol complex after being run through the FastRelax code |