CABS-dock: MHC2+RX8

Project name: MHC2+RX8

Status: done

submitted: 2025-12-30 09:33:03, status changed: 2025-12-30 23:53:30

Project settings

Protein sequence(s)	HAIKDHVISQFGAGDAFTDGELQSVGELMLADANQDDDWFELKMMEEFRAVDQDPYFVTPSVFCNTDETCQNVAHIFIDNGEFIQPTVKVAPPESRISNSNTITLMCLVTGFFPPEISITWFKNGQELTEGSTYTTNSVDEPADLFYDCKVNHQGTYEPMGLTVEEPGVQHFVHQFMYGEGSEVFDFDSDEYFYVDKRELGRPDAWVNGEVVPAELRSIQPAEHWDRNQLLEECRAHNGTLESVRVLLDRYYWNSQKESILRTRAVTMSCRHNYEIFVPPTVKVFPKPSIEKNGNVTLICLVTGFYPKHIEVKWLLNGQELPAQVGYYVNGSELQFQDALDDICPTVEKSGLYSCRVEHSGVFEPIGLEWEH input pdb
Peptide sequence	QEEINKIRAKIVEMN
Simulation mc cycles	50
Peptide secondary structure psipred	CHHHHHHHHHHHHCC

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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)	94.8073	1.06532	15.0383	101
cluster_2.pdb ( medoid)	46.2321	2.27115	32.446	105
cluster_3.pdb ( medoid)	30.6695	3.39099	13.3123	104
cluster_4.pdb ( medoid)	28.9245	4.52904	12.8877	131
cluster_5.pdb ( medoid)	28.2976	5.33615	19.8504	151
cluster_6.pdb ( medoid)	13.878	7.27771	21.5149	101
cluster_7.pdb ( medoid)	9.86764	10.4382	23.8614	103
cluster_8.pdb ( medoid)	9.73096	7.2963	31.0346	71
cluster_9.pdb ( medoid)	5.65551	10.9628	31.3315	62
cluster_10.pdb ( medoid)	4.99136	14.2246	36.8367	71