CABS-dock: pep2

Project name: pep2

Status: done

submitted: 2026-04-10 06:08:12, status changed: 2026-04-10 11:01:15

Project settings

Protein sequence(s)

GKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQL input pdb

Peptide sequence

VSEGKEKKGRLR

Simulation mc cycles

Peptide secondary structure psipred

CCCCCCCCCCCC

Flexible regions

61:A - 95:A

Contact information

61-95

Re-submit project

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)	26.8512	4.02217	30.035	108
cluster_2.pdb ( medoid)	18.9318	9.50784	32.1055	180
cluster_3.pdb ( medoid)	18.0365	6.09875	37.7718	110
cluster_4.pdb ( medoid)	17.1977	8.43134	31.7841	145
cluster_5.pdb ( medoid)	9.36602	12.5987	40.2798	118
cluster_6.pdb ( medoid)	8.01877	11.2237	26.7127	90
cluster_7.pdb ( medoid)	7.68696	8.32578	18.6221	64
cluster_8.pdb ( medoid)	5.28205	16.0922	38.8216	85
cluster_9.pdb ( medoid)	4.45042	13.9313	28.8631	62
cluster_10.pdb ( medoid)	3.22833	11.7708	27.4378	38