Structure Standby

In structure-based design/modeling, manipulation and curation of the macromolecule structure is usually the first step. Our Structure-Standby toolkit implements uploading and downloading structure files from the RCSB database, followed by the common options in molecular docking, molecular dynamics simulations, etc. Files in both pdb and cif format are supported.

Job name

Upload PDB file

max. 10MB
user-manual

Choose file

or

PDB code

Update
Advanced Options

Mutation string

Please enter the mutation string using residue index (not the PDB residue number), e.g. "1-GLN,4-ALA,5-LEU"

Extract by text

If checked, provide the selection of component using the MDAanlysis syntax, e.g. chainlD B

Extract by selection

If checked, the component selected in the above window will beextracted. Either extracted by text of selection. You can not checkboth boxes

Use the "reduce" program

If checked, the "reduce" program will be used to detect the protonation states of the ionizable residues. Default is not using reduce.

Add the missing atoms

If checked, the missing side-chain atoms will added, if there are residues missing side chains

Constantph

If checked, the residue name will be renamed to fit constant-pH MD simulations

Keep only the protein residues

If checked, the non-protein residues will be removed!

Load Example