As input Unres server can use protein sequence given using one letter code
(with XX to mark a new chain) or PDB files.
Only standard codes of aminoacids are recognized in PDB files.
PDB files can be downloaded from the PDB database based on given PDB code.
To select only a single chain use PDB_code:chain_id notation (for example
5G3Q:B), chain_id is case sensitive. For the PDB files containing multiple
models, only the first models is taken.
Unres server requires input PDB files with continuous (without breaks)
protein chains. PDB files with gaps in the structure have to be first prepared
by filling up all missing residues. There is a plan to add such service to
the UNRES server but currently, a user has to model missing fragment using
external software or online servers (for example Modeller software, Modloop
Disulfide bonds are read from PDB based on SSBOND records and for multichain
protein proper chain records are necessary. See example:
SSBOND 1 CYS C 107 CYS C 138
SSBOND 2 CYS C 124 CYS C 139
SSBOND 3 CYS C 137 CYS C 149
SSBOND 4 CYS D 107 CYS D 138
SSBOND 5 CYS D 124 CYS D 139
SSBOND 6 CYS D 137 CYS D 149
A protein structure with disulfide bonds and no corresponding
SSBOND records will result in clashes and a very high energy
which can crash calculations.
TER records in PDB file are read to recognize chain's ends.
Distance distribution (from SAXS experiment) can be added for MREMD
simulation in advanced mode. First column distance, second column
distribution function value (separated by space).
Secondary structure restraints can be added to MD and MREMD
simulation in advanced mode. Sequence of letters H,E and C or - for each
residue is used to input helical, extended and no restraints, respectively.
For MD simulations by default the snapshots are written in PDB format to be
displayed by NGLViewer. In advanced mode, the user can request the compressed
cx format, which is recommended for larger jobs. In this case, the movie
in mp4 and ogv formats are rendered and displayed. The movie files can also
be downloaded for further use.
For UNRES-dock simulations two pdb files or pdb codes with indication of
the chain letter are required. In case of protein-peptide docking,
sequence can be provided in one-letter format, instead of a structure
for peptide. User can also decide if restraints will be used for the
second molecule (ligand/peptide) during docking procedure. Standard of
the pdb files read by UNRES-dock is the same as for other UNRES