Model 3D structure of protein:

  • Archived Cases:

    Choose to run/view protein instances from the already archived cases
  • Job submission (simple):

    Supply distance bounds and dihedral angle bounds (if present) to model 3D structure
  • Job submission (expert):

    Supply input files as above and also algorithm specific parameters

Tutorial for running all the three modes below.

Simply Easy Learning DREAM accepts the amino acid sequence, distance bounds, and dihedral bounds (if available) as input. The experimental bounds are typically distributed across regions of relative abundance and paucity. DREAM models the data in the form of a graph such that regions of relative abundance form core substructures that appears as dense subgraphs. The core substructures are modeled separately and in parallel in a distance geometric framework, before consolidating them in a single step. The regions of paucity are modeled separately leading to an ensemble of structures. The native structure thus derived is dominantly driven by the experimental data. In order to model a structrue which is thermodynamically stable in solvent (water), energy minimization is carried only in the post processing stages to provide the final structure.

Stage1 Stage2 Stage3 Stage4
  • Read the input
  • Model in the form of a graph
  • find clusters with relatively larger
    concentration of experimental
    bounds.
  • Model three dimensional
    structure for the fragments
  • Consolidate the structures
    for the fragments
  • model structures for the
    regions with comparatively
    less number of bounds
  • Post process to get
    a thermodymically
    stable structure in
    solvent (water)

Archived Examples

  • The archived cases can be found here.
  • Parameters used for the archived cases can be found here.
  • The archived case can be re-run as well by selecting an entry from the drop-down menu.

  • Please choose from above from one of cases below


    Field marked with * is mandatory

    Job Submission (simple): Automatic parameter selection.

    • Email: *Protein name:
    • *Seq *Upl Aco
      Amino acid sequence (example). Upper bounds (example). Dihedral angle bounds (example).
    Fields marked with * are mandatory

    Job submission (expert): Manual parameter input.

    • Email: *Protein name:
    • *Seq *Upl Aco
      Amino acid sequence(example). Upper bounds(example). Dihedral angle bounds (example).
    • Input Parameters Archived Examples
      Hydrogen omission
      Augment bounds:
      Include neighbours:
      Break Graph: density-low
      density-high
      Multi Expand: k2
      Size cutoff
      Group min
      Increment min
      Group Expand
    Fields marked with * are mandatory