CABS-dock: PD1-DN-h

Project name: PD1-DN-h

Status: done

submitted: 2026-07-13 10:18:29, status changed: 2026-07-13 11:51:10

Project settings

Protein sequence(s)	NPPTFSPALLVVTEGDNATFTCSFSNTSSFVLNWYRMSPSNQTDKLAAFPECRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKLQIKESLRAELRVTERRA input pdb
Peptide sequence	DNWVDSSMDHNN
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCCCCCC

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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

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)	32.9857	7.09398	24.9253	234
cluster_2.pdb ( medoid)	24.1144	5.93007	17.9713	143
cluster_3.pdb ( medoid)	13.6505	8.35132	15.8841	114
cluster_4.pdb ( medoid)	11.6152	7.74845	28.0014	90
cluster_5.pdb ( medoid)	11.3647	7.91929	24.2133	90
cluster_6.pdb ( medoid)	8.993	9.1182	27.2229	82
cluster_7.pdb ( medoid)	7.80216	9.48455	22.6632	74
cluster_8.pdb ( medoid)	7.56673	9.91182	22.6366	75
cluster_9.pdb ( medoid)	6.65788	10.5139	35.8933	70
cluster_10.pdb ( medoid)	2.2712	12.3283	25.1755	28