Input data description:

  1. As input Unres server can use protein sequence given using one letter code (with XX to mark a new chain) or PDB files.
  2. Only standard codes of aminoacids are recognized in PDB files.
  3. 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.
  4. 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).
  5. 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
    
  6. A protein structure with disulfide bonds and no corresponding SSBOND records will result in clashes and a very high energy which can crash calculations.
  7. TER records in PDB file are read to recognize chain's ends.
  8. 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).
  9. 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.
  10. 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.
  11. 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.