CABS-dock: MHC2+RX

Project name: MHC2+RX

Status: done

submitted: 2025-12-30 09:31:02, status changed: 2025-12-30 18:19:39

Project settings

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

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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)	36.76	2.72035	4.42338	100
cluster_2.pdb ( medoid)	25.0877	2.39161	18.1618	60
cluster_3.pdb ( medoid)	24.9806	4.32336	26.2436	108
cluster_4.pdb ( medoid)	15.3631	12.172	61.8002	187
cluster_5.pdb ( medoid)	12.9664	12.8023	53.8347	166
cluster_6.pdb ( medoid)	9.34645	10.3783	20.915	97
cluster_7.pdb ( medoid)	7.40538	11.6132	56.6868	86
cluster_8.pdb ( medoid)	7.20631	14.5706	54.2258	105
cluster_9.pdb ( medoid)	5.73554	8.71757	25.0669	50
cluster_10.pdb ( medoid)	2.02664	20.2306	40.2557	41