UNRES server

Input data description:

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 server).

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).
New! 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.
New! 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:
1. 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).
2. 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:
  1. ZL - zero-length cross-links (invlving the basic and acidic groups of the protein, including the N- and the C-terminus).
  2. ADH - adypic acid dihydrazide, brignes Glu and Asp sidechains and the C-end carboxyl.
  3. PDH - pimelic acid dihydrazide, bridges Glu and Asp sidechains and the C-end carboxyl.
  4. DSS - disuccinylimidyl suberate, bridges the lysine sidechains.
3. 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:
  1. ADH - adipic acid dihydrazide, bridges Glu and Asp side chains (not the terminal carboxyl).
  2. PDH - pimelic acid dihydrazide, bridges Glu and Asp side chains (not the terminal carboxyl).
  3. BS2G - glutaric acid, bridges lysine side chains.
  4. BS3G - suberic acid, bridges lysine side chains.
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 simulations.