CABS-dock: YPLDMKVSL

Project name: YPLDMKVSL

Status: done

submitted: 2026-02-17 15:16:32, status changed: 2026-02-18 03:51:42

Project settings

Protein sequence(s)	GSHSSMMRYFFTSSVSRPGRGEEPRFIAVGYVDDTQFVRRFDSDAASQRMEEPRAPWIEQEGPPEYWDGETRRKVKAHHSSQTHRVDLGTLLRGYYNQSEAGSHTVQRRMYGCDVVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKKHHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQQRTDAPKKTHMTHHAVSDHEATLRCWALSSFYPPAEITLTTWQRRDGEDQTQDTELVEETRPAGDGTFQKKWAAVVVVPSSGQEQRYTCHVQHEGLPKPLTLRWQRRTPPKIQVVYSRHPAENGKSSNFLNCYVVSGFHPSDDIEVDLLKNGERIEKKVEHSDLSFSSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDDRD input pdb
Peptide sequence	YPLDMKVSL
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCCC

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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)	80.0296	2.02425	9.94933	162
cluster_2.pdb ( medoid)	74.6711	0.749955	3.13947	56
cluster_3.pdb ( medoid)	25.3527	4.02325	31.8416	102
cluster_4.pdb ( medoid)	25.2983	4.15047	23.539	105
cluster_5.pdb ( medoid)	14.0416	10.5401	42.7829	148
cluster_6.pdb ( medoid)	13.8774	11.0972	47.3847	154
cluster_7.pdb ( medoid)	13.7992	7.97148	47.5195	110
cluster_8.pdb ( medoid)	9.31701	6.43984	30.3245	60
cluster_9.pdb ( medoid)	9.08752	4.95185	15.1713	45
cluster_10.pdb ( medoid)	2.81427	20.6092	53.4864	58