CABS-dock: PEP1

Project name: PEP1

Status: done

submitted: 2026-04-10 05:36:10, status changed: 2026-04-10 10:08:41

Project settings

Protein sequence(s)

GKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQL input pdb

Peptide sequence

NLKSHESPERHEN

Simulation mc cycles

Peptide secondary structure psipred

CCCCCCCCCCCCC

Flexible regions

61:A - 95:A

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 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

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)	32.3328	6.95889	36.1142	225
cluster_2.pdb ( medoid)	22.5509	5.05523	38.0675	114
cluster_3.pdb ( medoid)	16.0585	8.90493	23.9427	143
cluster_4.pdb ( medoid)	14.639	7.24095	16.2478	106
cluster_5.pdb ( medoid)	10.975	7.38039	22.5301	81
cluster_6.pdb ( medoid)	9.60336	8.9552	20.9366	86
cluster_7.pdb ( medoid)	7.52272	9.571	24.4114	72
cluster_8.pdb ( medoid)	5.12345	9.95423	32.2745	51
cluster_9.pdb ( medoid)	4.85214	11.5413	27.6981	56
cluster_10.pdb ( medoid)	4.05603	16.2721	42.5073	66