HOWTO/How do I use this server?

How do I:

• run a molecular dynamics simulation of a protein/DNA/RNA?
  For proteins see the MD section of the UNRES tutorial, for DNA/RNA see that of the NARES tutorial.

• get an MD trajectory in the PDB format?
  Turn on the "trajectory as PDB" option in the input options; see the Canonical MD simulations of the Trp-Cage miniprotein section in the main tutorial.

• calculate the flexibility of my protein?
  Run a canonical MD simulation starting from the experimental structure. The output provides the fluctuations profile.

• model the structure and determine the ensemble averages of my system?
  For proteins (both monomeric and oligomeric) and peptides the best option is to use Multiplexed Replica Exchange; see the respective section of the tutorial.
  Restraints from bioinformatics predictions and experiment can be included. For nucleic acids only canonical MD is available at the moment, which does not enable ensemble modeling in a reasonable time except for small DNA/RNA molecules.

• include secondary-structure restraints?
  See the MREMD simulations of 5G3Q:B tutorial. Note that the tutorial has the condensed PSIPRED output; raw output which details the probabilities of coil, helix, and extended state is also available. See Input data description for more details.

• use templates from ColabFold/AlphaFold or other servers in the simulations?
  See the Input data description.

• include distance-distribution restraints from SAXS/SANS data?
  See the SAXS1#saxs1 or SAXS2 tutorial.

• include XL-MS (chemical cross-link mass spectroscopy) data?
  See the Input data description.

• include NMR-data restraints
  See the Input data description.

• model the conformations of a flexible protein if I have NMR data?
  You can run MREMD with time-average restraints. Please see the time average NMR tutorial.

• run calculations if my protein contains disulfide bridges?
  If you the disulfide-bridge topology is known and should remain as it is during the calculation (the only option in energy-minimization calculations), input the starting structure in the PDB format with (see the Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein section of the tutorial). If the disulfide-bridge topology is not known, use the "dynamic disulfide" option (MD/MREMD in advanced mode only).

• do peptide-protein or protein-protein docking?
  See the UNRES-Dock tutorial.

• determine the aggregation propensity of my peptide?
  See the peptide aggregation tutorial.