PDBrestore is a simple web interface for
repairing protein PDB chains extracted from a local PDB file or
a PDB file downloaded from
the Protein Data Bank .
PDBrestore adds the hydrogen atoms, the missing atoms of
side chains, fills the gaps in the sequence, produces the
itp parameters of a ligand according to
GAFF2 force
field , and produces a reasonably pre-equilibrated solvated
simulation BOX. The interface is aimed at alleviating the
cumbersome preparatory work for setting up a starting
protein+ligand coordinates PDB file to be used in drug design
projects (e.g. FEP or TI calculations of ligand binding affinities).
The interface can process only one protein chain at a time and supports only protein-ligand systems . DNA or RNA chains are not supported. PDBrestore as a command-line application is available in the ORAC distribution.