PDBrestore is a simple web interface for
repairing protein PDB chains extracted from a PDB file downloaded
from the Protein Data Bank of
from a local PDB file in standard format including the SEQRES
lines. 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.