CABS-dock: Nirbhay-V8_protease-Pteroicidin-Alpha-DOCK

Project name: Nirbhay-V8_protease-Pteroicidin-Alpha-DOCK

Status: done

submitted: 2025-06-21 17:26:14, status changed: 2025-06-21 21:03:25

Project settings

Protein sequence(s)	VILPNNDRHQITDTTNGHYAPVTYIQVEAPTGTFIASGVVVGKDTLLTNKHVVDATHGDPHALKAFPSAINQDNYPNGGFTAEQITKYSGEGDLAIVKFSPNEQNKHIGEVVKPATMSNNAETQTNQNITVTGYPGDKPVATMWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVPNEFNGAVFINENVRNFLKQNIEDINFA input pdb
Peptide sequence	FIHHIIGGLFHVGKSIHDLIR
Simulation mc cycles	50
Peptide secondary structure psipred	CCHHHHHHHHHHCHHHHHHHC

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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)	46.9067	3.70949	14.0448	174
cluster_2.pdb ( medoid)	26.6389	5.89364	36.9465	157
cluster_3.pdb ( medoid)	17.9713	7.51196	37.6378	135
cluster_4.pdb ( medoid)	8.46733	11.1015	30.2907	94
cluster_5.pdb ( medoid)	7.03211	9.38552	28.4744	66
cluster_6.pdb ( medoid)	6.86881	16.0144	39.9754	110
cluster_7.pdb ( medoid)	6.61835	14.5051	32.7053	96
cluster_8.pdb ( medoid)	5.72179	10.3115	24.5704	59
cluster_9.pdb ( medoid)	5.03109	12.5221	42.2007	63
cluster_10.pdb ( medoid)	2.28098	20.1668	41.7335	46