CABS-dock: ComD

Project name: ComD

Status: done

submitted: 2025-11-12 16:24:14, status changed: 2025-11-13 06:24:46

Project settings

Protein sequence(s)	MDLFGFGTVIVHFLIISHSYHFICKGQINRKELFVFGAYTLLTEIVFDFPLYILYLDGLGIERFLFPLGLYSYFRWMKQYERDRGLFLSLLLSLLYESTHNFLSVTFSSITGDNFVLQYHFPFFFVVTVLTYFVTLKIIYYFHLELAYFDEDYLYPFLKKVFFALLLLHIVSFVSDMVSTIKHLNSFGSILSSIVFISLLMDLFGFGTVIVHFLIISHSYHFICKGQINRKELFVFGAYTLLTEIVFDFPLYILYLDGLGIERFLFPLGLYSYFRWMKQYERDRGLFLSLLLSLLYESTHNFLSVTFSSITGDNFVLQYHFPFFFVVTVLTYFVTLKIIYYFHLELAYFDEDYLYPFLKKVFFALLLLHIVSFVSDMVSTIKHLNSFGSILSSIVFISLL input pdb
Peptide sequence	EMRLSAFFRDFILQRKK
Simulation mc cycles	50
Peptide secondary structure psipred	CCCHHHHHHHHHHHHCC

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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)	103.27	0.968335	2.38711	100
cluster_2.pdb ( medoid)	49.5967	1.97594	21.081	98
cluster_3.pdb ( medoid)	47.1821	2.33139	12.1242	110
cluster_4.pdb ( medoid)	26.794	3.80682	15.4767	102
cluster_5.pdb ( medoid)	22.6374	6.53785	18.1237	148
cluster_6.pdb ( medoid)	20.6091	5.87118	14.5649	121
cluster_7.pdb ( medoid)	12.4869	8.72912	17.8508	109
cluster_8.pdb ( medoid)	8.40621	9.7547	19.8513	82
cluster_9.pdb ( medoid)	6.12999	14.0294	36.758	86
cluster_10.pdb ( medoid)	5.98752	7.34862	15.3411	44