CABS-dock: 4DVY-Third

Project name: 4DVY-Third_sequence

Status: done

submitted: 2026-04-19 12:52:00, status changed: 2026-04-19 15:12:44

Project settings

Protein sequence(s)	QQFINNLQVAFIKVDNVVASFDPDQKPIVDKNDRDNRQAFDGISQLREEYSNKAIKNPTKKNQYFSDFIDKSNDLINKDNLIDVESSTKSFQKFGDQRYQIFTSWVSMQKDPSKINTRSIRNFMENIIQPPIPDDKEKAEFLKSAKQSFAGIIIGNQIRTDQKFMGVFDESLKERQEAEKNGGPTGGDWLDIFLSFIFALSSVLMGSHNGIEKVSLLYAGNGGFGDKHDWNATVGYKNVATLINVHMKNGSGLVIAGGEKGINNPSFYLYKEDQLTGSQRALSQEEIRNKVDFMEFLAQNNTKLDNLSEKEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEFNNGDLSYTLKDYNVTLQGSLKHDGVMFVDYSFNKVAVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDFLSSNKELAGKALNFNKAVAEAKSTGNYDEVKKAQKDLEKSLRKREHLEKEVEKKLESKSNKMEAKAQANSQKDEIFALINKEANRDARAIAYTQNLKGIKRELSDKLEKISKDLKDFSKSFDEFKEETLKALKGSVKDLGINPEWISKVENLNAALNEFKNFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVSVAKAMGDFSRVEQVLADLKNFSKEQLA input pdb
Peptide sequence	GLLKKIKWLL
Simulation mc cycles	5
Peptide secondary structure psipred	CHHHHHHHHC

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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

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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)	37.6959	2.65281	10.9008	100
cluster_2.pdb ( medoid)	26.579	2.03168	4.09346	54
cluster_3.pdb ( medoid)	16.3992	6.09786	13.6458	100
cluster_4.pdb ( medoid)	15.9393	2.94868	23.1445	47
cluster_5.pdb ( medoid)	12.2027	14.3411	33.696	175
cluster_6.pdb ( medoid)	9.35434	11.6523	65.4116	109
cluster_7.pdb ( medoid)	8.32731	13.9301	34.5902	116
cluster_8.pdb ( medoid)	7.1933	4.44858	25.0719	32
cluster_9.pdb ( medoid)	6.8741	11.9288	32.2242	82
cluster_10.pdb ( medoid)	6.27067	12.2794	29.9815	77