CABS-dock: VKACPGGY

Project name: VKACPGGY

Status: done

submitted: 2026-02-17 15:16:14, status changed: 2026-02-18 03:47:14

Project settings

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

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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)	49.3548	1.45883	5.87529	72
cluster_2.pdb ( medoid)	41.3278	2.61325	9.87148	108
cluster_3.pdb ( medoid)	36.514	2.87561	10.9879	105
cluster_4.pdb ( medoid)	27.0226	2.92347	15.8613	79
cluster_5.pdb ( medoid)	19.7555	5.66931	22.9113	112
cluster_6.pdb ( medoid)	15.1259	8.39619	45.4565	127
cluster_7.pdb ( medoid)	13.4983	13.8536	44.187	187
cluster_8.pdb ( medoid)	9.82664	11.8046	41.2098	116
cluster_9.pdb ( medoid)	4.61667	14.5126	33.8562	67
cluster_10.pdb ( medoid)	2.76677	9.75866	23.9705	27