CABS-dock: MHC-I

Project name: MHC-I_SEAVAKKMF

Status: done

submitted: 2025-12-30 09:52:27, status changed: 2025-12-31 15:34:39

Project settings

Protein sequence(s)	VLLNTVSAATNTLQYFYTATSGIDNFPEFVTMGIVNGHQIDHYDSITKRAIQKAEWISGAVDPDYWKRNTQTYAAEEPVFLNNIKIAKSRFNQTGGVHTNQRMYGCEWNDETGATGGYFQDGYDGEDFIAFDLKTKTWIAPKPQAVITKLKWDSDIAMTEQKKHYLTQECIEWLKKYLDYGKSTLMTTVPPSVTLLQKTPSSPVTCHATGFYPSGVMVFWQKDGQDQHGDVEHGETLPNDDGTFQKSTHLTLTPEEWKKKQYQCVVQVTGIKEDFIKVLTESEIKTNWNNPAPNIVLIIGVVVALLLVIVAVVGVVIWKKKSKKGFIQAQSSDTDSDNSGRAAQQIMKSILSIVVLGLIYSAVEAKESPPKVQVYSRNPGNFGDKNTLICHVSGFHPPDISIQLLKNGVEIPDAKQTDLAFEQGWQFHLTKSVGFTPASGEEYTCRVRHLKNLKTYTWEADM input pdb
Peptide sequence	SEAVAKKMF
Simulation mc cycles	100
Peptide secondary structure psipred	CHHHHHHHC

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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)	25.8689	4.1749	33.5151	108
cluster_2.pdb ( medoid)	20.1909	6.24042	29.9889	126
cluster_3.pdb ( medoid)	18.4443	6.28921	16.2381	116
cluster_4.pdb ( medoid)	17.0176	11.5763	44.4873	197
cluster_5.pdb ( medoid)	11.0735	6.0505	23.8899	67
cluster_6.pdb ( medoid)	9.79077	9.49874	22.7088	93
cluster_7.pdb ( medoid)	7.01929	17.0958	43.8515	120
cluster_8.pdb ( medoid)	5.63321	9.586	22.9755	54
cluster_9.pdb ( medoid)	5.59951	11.9653	39.2626	67
cluster_10.pdb ( medoid)	4.54872	11.4318	27.748	52