Data
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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
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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
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Number of Alignments
Number of desired alignments.
All vs All
One vs All
The One
Select surface/molecule to be aligned with all others.
*Hover over field names for more information.
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