CABS-dock: PEPTIDE3

Project name: PEPTIDE3

Status: done

submitted: 2025-07-02 09:25:03, status changed: 2025-07-02 13:48:59

Project settings

Protein sequence(s)	EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTN input pdb
Peptide sequence	FFNKKNK
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCC

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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)	35.5142	2.87209	9.26807	102
cluster_2.pdb ( medoid)	26.1605	5.58093	29.4611	146
cluster_3.pdb ( medoid)	25.8309	3.7939	8.64219	98
cluster_4.pdb ( medoid)	12.0265	8.81385	24.165	106
cluster_5.pdb ( medoid)	11.6589	10.0353	25.8369	117
cluster_6.pdb ( medoid)	11.5156	10.768	28.4822	124
cluster_7.pdb ( medoid)	9.52291	11.8661	31.8789	113
cluster_8.pdb ( medoid)	8.01909	9.9762	24.6488	80
cluster_9.pdb ( medoid)	6.89519	10.5871	24.0581	73
cluster_10.pdb ( medoid)	3.82855	10.709	31.4974	41