CABS-dock: VKACPGGY

Project name: VKACPGGY - b

Status: done

submitted: 2026-02-17 15:27:21, status changed: 2026-02-18 08:49:12

Project settings

Protein sequence(s)	QPVLHQPPAMSSALGTTIRLTCTLRNDHDIGVYSVYWYQQRPGHPPRFLLRYFSQSDKSQGPQVPPRFSGSKDVARNRGYLSISELQPEDEAMYYCAMGARSSEKEEREREEVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARHYYYYYGMDVWGQGTTVTVSSWSASAPTLFPLVSCVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVTDEHVVCKVQHPNGNKEKNVPLPSVTHVFGSGTQLTVLSQPKATPSVTLFPPSSEELQANKATLVCLMNDFYPGILTVTWKADGTPITQGVEMTTPSKQSNNKYAASSYLSLTPEQWRSRRSYSCQVMHEGSTVEKTVAP 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 3Dmol (WebGL)

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)	27.8929	3.72855	22.9804	104
cluster_2.pdb ( medoid)	16.4598	7.10823	36.7007	117
cluster_3.pdb ( medoid)	12.062	12.4357	43.2782	150
cluster_4.pdb ( medoid)	11.2941	11.6875	32.2216	132
cluster_5.pdb ( medoid)	11.0374	8.15409	25.2949	90
cluster_6.pdb ( medoid)	8.13103	13.6514	42.3394	111
cluster_7.pdb ( medoid)	6.00685	19.3113	47.7297	116
cluster_8.pdb ( medoid)	5.76433	14.2254	34.1092	82
cluster_9.pdb ( medoid)	4.05849	12.5663	31.9466	51
cluster_10.pdb ( medoid)	3.20528	14.6633	43.1016	47