Receptor Molecule:
A file containing the structure of the receptor in OPM output PDB format.
Each residue of the receptor must have a unique number and chain.
The default is the whole complex(All). For specific chains please write chains Id with commas in between (A,B...).
Ligand Molecule:
A file containing the structure of the ligand in OPM output PDB format. Each residue of the receptor must have a unique number and chain. sThe default is the whole complex(All). For specific chains please write chains Id with commas in between (A,B...).
We recommend defining the smaller protein as the ligand, for better rigid-body minimization
e-mail address:
An e-mail address for receiving the results.
Setting these parameters is optional:
- Perform SCO for:
Unchecking the boxes will keep side-chains of the molecule fixed
- SCO Level: Restricted or Full.
The restricted refinement mode allows only the clashing residues to be flexible.
The full refinement mode allows all the interface residues to be flexible and uses an extended rotamer library.
We recommend using the restricted mode at first, for coarse refinement,
and on the final best candidates to use the full mode.
- Number of normal modes: The maximal number of low frequency normal modes that the program will use in the refinement.
This parameter determined the amount of degrees of freedom of the backbone conformation, that the program will take into account during the refinement.
However, the lower this value is, the faster the program will run.
For example, if this parameter is set to 50, the program will refine the structure of the receptor by the most relevant normal modes among the 50 lowest frequency modes.
- Backbone flexibility level: This parameter determines the restriction of the backbone conformational change.
The lower it is, the more it prevents the backbone conformation to deform.
The flexibility level must be between 0 and 1.
The results will be sent via email (compressed file).
The first 20 sorted docking candidates PDB files will be sent.
The output file "memdock.csv" is a table of all the output docking candidates, ranked by the Memscore.
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