CABS-dock: all_three

Project name: all_three_iter1-iter2

Status: done

submitted: 2025-12-28 20:50:22, status changed: 2025-12-29 06:21:14

Project settings

Protein sequence(s)	SSVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIETDRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKGDYMNM input pdb
Peptide sequence	NEDKELCGSHLVDMLPDYCGERGFFYSPHK
Simulation mc cycles	50
Peptide secondary structure psipred	CCCHHHHHHHHHHHCHHHCCCCCCCCCCCC

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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)	29.8106	3.45515	7.19057	103
cluster_2.pdb ( medoid)	24.0121	4.53938	20.8088	109
cluster_3.pdb ( medoid)	18.1672	8.80711	26.7981	160
cluster_4.pdb ( medoid)	14.7545	7.18427	20.2152	106
cluster_5.pdb ( medoid)	12.0852	9.01928	22.7348	109
cluster_6.pdb ( medoid)	11.1957	8.48543	27.3628	95
cluster_7.pdb ( medoid)	10.0132	8.98811	16.3398	90
cluster_8.pdb ( medoid)	9.57723	11.2768	24.5348	108
cluster_9.pdb ( medoid)	6.1022	15.2404	31.7704	93
cluster_10.pdb ( medoid)	2.06241	13.0915	24.9882	27