Identification of Flexible Layers

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An anchor segment is selected from the rigid segments in an automatic fashion (see see Manual Specification of Non-rotatable Bonds to override this behavior). The molecule is divided into segments that overlap at each rotatable bond. The segment with the largest number of heavy atoms is selected as the anchor. All segments with more heavy atoms then min_anchor_size are tried separately as anchors.

Overlapping segments.jpg
  • Identification of overlapping segments

When an anchor has been selected, then the molecule is redivided into non-overlapping segments, which are then arranged concentrically about the anchor segment. Segments are reattached to the anchor according to the innermost layer first --and within a layer--the largest segment first.

Layered segments.jpg
  • Identification of Layered Segments

The anchor is processed separately (either oriented, scored, and/or minimized). The remaining segments are subsequently re-attached during the conformation search. The interaction energy between the receptor and the ligand can be optimized with a simplex minimizer (see Minimization).