CABS-dock: 9) AMP

Project name: 9) AMP_BRELA

Status: done

submitted: 2026-01-14 11:44:21, status changed: 2026-01-14 16:29:09

Project settings

Protein sequence(s)	MSRIILFAAILAIIAVSANGASNLPALDMASIPDEYKDLVPPEVTTFYNELTEDDKKILKEVAEKHSEYATDEDALNALKEKSEKLYTKANELRNLVKDRISKLNPEAKTFVDTIIEKLKALRPKEDEKPNLTELRKEANEIVEKFKALSEEAKESLKTNFPKITGVIQNEKFQKLAQSLLKPEGAAAPA input pdb
Peptide sequence	LYKLVKVVLNM
Simulation mc cycles	50
Peptide secondary structure psipred	CCHHHHHHHCC

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Zoom/rotate predicted model of the complex using mouse. Click the "View" button on the right panel to load the appropriate model. View in JSmol (pure html5/js) if you got rendering problems.

Models are ranked and numbered according to their occurrence in docking trajectory (1 = most probable result).

Representative conformations

	model_1		Download
	model_2		Download
	model_3		Download
	model_4		Download
	model_5		Download
	model_6		Download
	model_7		Download
	model_8		Download
	model_9		Download
	model_10		Download

Download all files

Click the "View" button to load the contact map of appropriate model.

Representative conformations

Contact cutoff (Å)

	model_1	View
	model_2	View
	model_3	View
	model_4	View
	model_5	View
	model_6	View
	model_7	View
	model_8	View
	model_9	View
	model_10	View

Receptor residue	Peptide residue

Receptor residue	Peptide residue

Receptor residue	Peptide residue

Select trajectory from the right panel to display animation in JSmol. Note that it may hangs browser window for few minutes or ever.

Trajectories

	replica_1		Download
	replica_2		Download
	replica_3		Download
	replica_4		Download
	replica_5		Download
	replica_6		Download
	replica_7		Download
	replica_8		Download
	replica_9		Download
	replica_10		Download

Selected model: model_1.pdb (most representative model of the best cluster) download the model

Details about clusters

cluster name	cluster density	average rmsd	max rmsd	number of elements
cluster_1.pdb ( medoid)	58.9419	3.32531	21.3197	196
cluster_2.pdb ( medoid)	51.5268	2.1154	5.12505	109
cluster_3.pdb ( medoid)	35.6657	3.00008	39.011	107
cluster_4.pdb ( medoid)	32.7453	4.70297	20.4659	154
cluster_5.pdb ( medoid)	23.0515	5.33587	30.626	123
cluster_6.pdb ( medoid)	19.7949	3.08161	21.6796	61
cluster_7.pdb ( medoid)	8.94038	9.39557	28.0694	84
cluster_8.pdb ( medoid)	7.76789	11.0712	33.1054	86
cluster_9.pdb ( medoid)	6.92535	3.46553	27.9724	24
cluster_10.pdb ( medoid)	4.20559	13.3156	31.2757	56