CABS-dock: NanAmid

Project name: NanAmid

Status: done

submitted: 2026-05-01 08:18:51, status changed: 2026-05-01 21:06:26

Project settings

Protein sequence(s)	GAALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSKDL input pdb
Peptide sequence	DSGYEVHHQKLVFFAEDVGSNKGAIIGLM
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCEEEECEEEEEEEECCCCCCEEEECC

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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

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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)	36.4015	2.4999	5.27286	91
cluster_2.pdb ( medoid)	26.1098	4.25128	22.2708	111
cluster_3.pdb ( medoid)	13.2114	5.52553	11.475	73
cluster_4.pdb ( medoid)	12.1211	13.6951	30.0588	166
cluster_5.pdb ( medoid)	12.0714	13.503	33.2537	163
cluster_6.pdb ( medoid)	7.42595	14.8129	44.1241	110
cluster_7.pdb ( medoid)	7.28675	10.7044	33.5063	78
cluster_8.pdb ( medoid)	3.75354	13.0544	35.5788	49
cluster_9.pdb ( medoid)	2.89165	17.2912	32.0091	50
cluster_10.pdb ( medoid)	2.60278	3.45784	5.32079	9