Tutorial

1. Choose one from the dropdown list.
2. Type your email address in the space provided.
3. Click submit. The page proceeds only if email field in not empty.
4. The results are mailed after completion of successful run.
5. The mail would also contain a link to view a result.

1. Parameters used for the tested cases can be found here.

1. Type your email address in the space provided.
2. Supply your own:
   1. Amino acid sequence files in CYANA format (see example) or download from BMRB restraints grid (see example).
   2. Distance bounds files in CYANA format (see example) or download from BMRB restraints grid (see example). In case of multiple files (e.g. NOESY distance bounds and HBond files), concatenate into a single file.
   3. (Optional) Dihedral angle bounds files in CYANA format (see example) or download from BMRB restraints grid (see example). In case of multiple files (e.g. NOESY distance bounds and HBond files), concatenate into a single file.
3. Click submit. The page proceeds only if email field in not empty.
4. The results are mailed after completion of successful run.
5. The mail would also contain a link to view a result.

1. Type your email address in the space provided.
2. Supply your own:
   1. Amino acid sequence files in CYANA format (see example) or download from BMRB restraints grid (see example).
   2. Distance bounds files in CYANA format (see example) or download from BMRB restraints grid (see example). In case of multiple files (e.g. NOESY distance bounds and HBond files), concatenate into a single file.
   3. (Optional) Dihedral angle bounds files in CYANA format (see example) or download from BMRB restraints grid (see example). In case of multiple files (e.g. NOESY distance bounds and HBond files), coctatenate into a single file.
3. Select augment bounds (0 or 1): appends additional distance constraints using triangle inequality.
4. Select include neighbours (integers): expanding divided fragment to include residues if certain number of experimental distance bounds exists between the fragment and the residue(s) being included.
5. Select break graph at (0.1-1): controls the fragments during the divide stage.
6. Select group expand (integers): expanding divided fragment to include atoms if certain number of experimental distance bounds exists between the fragment and the residue(s) being included.
7. Click submit. The page proceeds only if email field in not empty.
8. The results are mailed after completion of successful run.
9. The mail would also contain a link to view a result.

1. On completion an email is sent to the email address provided.
2. It contains .pdb files along with a report file for each of the .pdb files.
3. A link is also provided to view the files.

Protein structure files (PDB format)

1. Individual files in PDB format for all the five models.
2. Ensemble file containing all the models aligned together.

Experimental distance violations

1. Distance violations for each of the five models are displayed (one shown here).
2. Experimental distance costraints are categorised into strong (0-2.7Å), medium (2.7-3.5Å) and weak (3.5-6Å).
3. Distance violations are reported for each of the categories, arranged in ascending order.

Ramachandran plot

1. Distance violations for each of the five models are displayed (one shown here).

Progress for DREAM (archived examples and expert mode with parameters supplied)

1. Progress of the DREAM algorithm, for running archived examples of expert mode with parameters supplied by the user.
2. Steps such as "divide and model", "model gaps", "gap correct" and "post processing" steps proceeds in parallel.
3. Various nodes in the graph are colour coded as green (success), orange (steps did not complete) and red (failoure).

Progress for DREAM (simple-expert mode)

1. Progress of the DREAM algorithm, for running in expert mode (simple).
2. Four parameters were predicted to model the structure for the protein, namely "Param-1", "Param-4", "Param-6", "Param-7" and "Param-8"
3. Using the parameter set in "Param-1", "Param-7" and "Param-8", were able to model structure for the fragment having divided the protein into regions having larger concentration of experimental bounds
4. However, DREAM choose the parameter set, i.e., "Param-1" which gives largest coverage of the protein with fewer outliers in the ramachandran plot.
5. Note that after parameter set "Param-1" is chosen, computation for other parameter set is stopped.
6. Steps such as "divide and model", "model gaps", "gap correct" and "post processing" steps proceeds in parallel.
7. Various nodes in the graph are colour coded as green (success), orange (steps did not complete) and red (failoure).

1. Go to BMRB site.
2. Select a protein by searching with its PDB ID. Click submit.

1. Click to show all the files.

1. Find the files corresponding to DYANA/DIANA (same as CYANA).