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    Data

  • Input Files
    The input molecules/surfaces. Molecules are expected in PDB format. Surfaces are expected in OFF format. All files must be of same type.

    Surface Type
    If input is molecules, then a surface of interest is computed.
    Choices are the molecular skin surface (full) of the molecule, the surface of a ligand (ligand), or part of the skin surface close to a ligand (binding).
    The user is expected to select the ligand (if needed) in a subsequent form.

    Recommended parameters for each type are filled in automatically.
    Full Ligand Binding
    • *Hover over field names for more information.

    Parameters

  • Curvature Radius
    Curvature is computed by averaging a local estimate of the curvature tensor around a neighborhood of each vertex. This parameter captures the neighborhood size in Angstroms.

    Simplification Threshold
    The Morse-Smale complex of mean curvature is simplified to retain significant maxima representing significant protrusions. This threshold indicates what fraction of the maximum mean curvature is deemed to be insignificant.

    Multi-Scale correspondence threshold
    Significant protrusions are matched across a pair of surfaces by comparing the curvatures at multiple scales. This threshold indicates what fraction of the maximum mean curvature over all scales should be accepted as a correspondence.

    Maximum relative distance
    A pair of correspondences are said to be consistent with each other if their pairwise distances are similar. For example, if (a,a') and (b,b') are two correspondances , where a,b are on one surface and a',b' are on the other, they are consistent with each other if |d(a,b) - d(a',b') | is less than Tmrd (in Angstroms).
    • *Hover over field names for more information.

    Options

  • Number of Alignments
    Number of desired alignments.

    All vs All One vs All
    • *Hover over field names for more information.