CABS-dock: PD1-MR-h

Project name: PD1-MR-h

Status: done

submitted: 2026-07-13 10:18:57, status changed: 2026-07-13 11:52:45

Project settings

Protein sequence(s)	NPPTFSPALLVVTEGDNATFTCSFSNTSSFVLNWYRMSPSNQTDKLAAFPECRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKLQIKESLRAELRVTERRA input pdb
Peptide sequence	MDRPGNTYNVGR
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 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)	23.808	4.7883	18.5949	114
cluster_2.pdb ( medoid)	21.0137	4.99673	17.6024	105
cluster_3.pdb ( medoid)	19.2179	8.16946	25.2847	157
cluster_4.pdb ( medoid)	17.7355	5.3001	30.9883	94
cluster_5.pdb ( medoid)	14.8895	9.80559	27.4611	146
cluster_6.pdb ( medoid)	13.8916	11.0138	24.8345	153
cluster_7.pdb ( medoid)	7.3167	10.6605	33.3301	78
cluster_8.pdb ( medoid)	7.27708	9.48182	21.549	69
cluster_9.pdb ( medoid)	6.3804	4.54517	16.2884	29
cluster_10.pdb ( medoid)	5.63196	9.76569	32.7418	55