Identification of Flexible Layers - Revision history

Frodo at 09:55, 13 March 2014

2014-03-13T09:55:13Z

← Older revision		Revision as of 09:55, 13 March 2014
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	* Identification of Layered Segments		* 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).		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).

			[[Category:Docking]]

Therese: 2 revisions

2012-10-08T20:27:50Z

2 revisions

← Older revision	Revision as of 20:27, 8 October 2012
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Frodo at 22:48, 22 September 2006

2006-09-22T22:48:19Z

← Older revision		Revision as of 22:48, 22 September 2006
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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.		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.
			[[Image:Overlapping_segments.jpg\|center]]
	~~(picture):~~ Identification of overlapping segments		* 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.		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.
			[[Image:Layered_segments.jpg\|center]]
	~~(picture) :~~Layered ~~non-overlapping segments~~		* 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).		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).

JohnIrwin at 22:39, 19 September 2006

2006-09-19T22:39:23Z

New page

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.

(picture): 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.

(picture) :Layered non-overlapping 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).