CABS-dock: Naktide

Project name: Naktide_SRC

Status: done

submitted: 2025-05-09 01:43:23, status changed: 2025-05-09 11:15:50

Project settings

Protein sequence(s)	VTTFVALYDYESRTETDLSFKKGERLQIVNNTRKVDVSQTWFTFRWLQREGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLACKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQPGENL input pdb
Peptide sequence	SATWLALSRIAGLCNRAVFQ
Simulation mc cycles	50
Peptide secondary structure	CCHHHHHHCCCCCCCCCCCC

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 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)	22.7098	5.59229	27.1392	127
cluster_2.pdb ( medoid)	22.6959	5.86009	26.584	133
cluster_3.pdb ( medoid)	21.4757	4.9358	30.0527	106
cluster_4.pdb ( medoid)	11.6692	13.5399	44.7265	158
cluster_5.pdb ( medoid)	7.48468	14.1623	41.0312	106
cluster_6.pdb ( medoid)	6.7217	18.894	40.756	127
cluster_7.pdb ( medoid)	6.31341	15.8393	33.4642	100
cluster_8.pdb ( medoid)	5.04886	8.51677	25.4939	43
cluster_9.pdb ( medoid)	3.91735	10.211	29.6004	40
cluster_10.pdb ( medoid)	2.73106	21.9695	48.1511	60