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As input Unres server can use protein sequence given using one letter code
(with XX to mark a new chain) or PDB files.
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Only standard codes of aminoacids are recognized in PDB files.
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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.
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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
server).
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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.
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TER records in PDB file are read to recognize chain's ends.
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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).
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Interproton-distance restraints and restraints on the phi and psi backbone
dihedral angles can now be included. This feature is available in the advanced mode.
The restraints are available in the NEF format (which is becoming the standard), in the
NMR-star format or in
the text format. The text-format files have the following structure:
phi 4 -88.2 -48.2
psi 4 -59.2 -19.2
phi 5 -84.8 -44.8
psi 5 -57.3 -17.3
phi 6 -86.6 -46.6
psi 6 -58.9 -18.9
....
49 79 1 5.0 HD1 H
49 12 1 5.0 HD1 H
4 52 2 5.0 HD1 H
4 59 2 5.0 HD1 H
....
In the angular section, the angle is marked "phi" or "psi", which is followed by residue index and the lower and upper angle boundary.
In the distance section, the first two numbers are the indices of the residues followed by peak index (the peak is ambiguous if the index is repeated in several lines), the upper distance boundary and proton types.
From the menu the user can select the following items of equations 3 and 4 in Lubecka and Liwo, J.Comput.Chem., 43, 2047 (2022) scaling factor in the log-exp ambiguous-restraint penalty function (scal_peak; factor alpha in equation 3), restraint well-depth (fordepth_peak; factor A in equation 4), and the slope of the flat-top part of the penalty function (slope_peak; factor kappa in equation 4). See Lubecka and Liwo, J.Comput.Chem., 43, 2047 (2022) for details.
Use of NMR restraints requires the use of the scale-consistent NEWCT-9P variant of UNRES.
- Chemical cross-link restraints. These can be input in three formats: Calpha-Calpha contact restraints, in which the flat-bottom bounded contact function of equation 3 of Lubecka and Liwo J. Comput. Chem. 40, 2164 (2019), statistical pseudopotentials (Fajardo et al., Proteins, 87, 1283 (2019) parameterized based on the Calpha-distance distributions determined by Leitner and colleagues (Leitner et al., PNAS, 111, 9455 (2014) or the pseudopotentials determined by MD simulations (Kogut et al., J Comput Chem. 42, 2054 (2021)). The crosslink type is selected by clicking the appropriate button. The format is the following:
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Contact-type crosslinks:
...
2 5 2.5 8.0 1 1.0 1.0
2 6 2.5 8.0 1 1.0 1.0
3 6 2.5 8.0 1 1.0 1.0
...
where the first two integers are residue indices. If the first residue is not glycine, add 1 to each index according to UNRES style, in which the first residue is a dummy if the first full residue is not glycine. The next two numbers are the lower and the upper distance bouundary. The next integer is 1 for sidechain-sidechain contacts and 0 for Calpha-Calpha contacts. The last two numbers are the well depth and well-wall breadth of the flat-bottom bounded restraint function (constants A and sigma in equation 3 of Lubecka and Liwo, J. Comput. Chem., 40, 2164 (2019).
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Leitner statistical pseudopotentials:
...
DSS ilink=39 jlink=53 score=15
DSS ilink=39 jlink=88 score=15
DSS ilink=5 jlink=39 score=15
...
The first item is crosslink identifier, the next two items are the indices of the bridged residues (1 added if the first residue is not glycine), the last item is the scaling factor of the pseudopotential. The following bridges are available:
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ZL - zero-length cross-links (invlving the basic and acidic groups of the protein, including the N- and the C-terminus).
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ADH - adypic acid dihydrazide, brignes Glu and Asp sidechains and the C-end carboxyl.
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PDH - pimelic acid dihydrazide, bridges Glu and Asp sidechains and the C-end carboxyl.
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DSS - disuccinylimidyl suberate, bridges the lysine sidechains.
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MD-determined pseudopotentials.
...
ilink=39 jlink=53 bridge=BS3
ilink=25 jlink=27 bridge=BS3
...
The first and the second item are the indices of cross-linked residues (add 1 if the first residue is not glycine), the last is cross-link type.
The following bridges are available:
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ADH - adipic acid dihydrazide, bridges Glu and Asp side chains (not the terminal carboxyl).
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PDH - pimelic acid dihydrazide, bridges Glu and Asp side chains (not the terminal carboxyl).
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BS2G - glutaric acid, bridges lysine side chains.
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BS3G - suberic acid, bridges lysine side chains.
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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.
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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.
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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
simulations.
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New!
Time-averaged functionality of NMR-data-assisted simulations has been
included, following the spirit of NMR measurements, which return
time-averaged observables thus corresponding to ensembles rather than to
particular structure. The time-averaged restraints are available
in the advance mode of MD and MREMD, 1 to 4 reference structures
can be used is simulations.
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New!
Template based restraints are added in Basic and Advanced modes of MREMD
simulations. Zip file can include up to 50 pdb files.
Other files in zip file are ignored and zip
files from ColabFold AlphaFold2 server can be used without any changes
to provide restraints. Restraint residues are selected based on confidence
factor read from bfactor field in pdb files. Each chain in multichain
protein can be restraint seperately or
template based restraints can span all chains.
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New!
Secondary structure restraints using SS2 VFormat from Psipred
for MD and MREMD simulations:
1 T C 0.999 0.000 0.003
2 T E 0.374 0.004 0.544
3 Y E 0.078 0.004 0.899
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New!
Peptide aggregation (MREMD mode only); only the sequence of a single peptide chain and peptide
concentration are required in the basic mode; the number of peptide molecules
in a box is assumed to be 8. This number can be changed in the advanced mode,
in which also advanced MREMD settings can be entered.
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New!
Coarse-grained DNA and RNA simulations. Energy minimization and canonical MD
can be run at the moment, only basic mode enabled.