CABS-dock: published binder 25mer 2nd

Project name: published binder 25mer 2nd

Status: done

submitted: 2026-04-02 15:43:34, status changed: 2026-04-02 17:53:18

Project settings

Protein sequence(s)	SMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMMSQNFTNNCCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEEGSVANKFYYVHNDIFRYQDEVF input pdb
Peptide sequence	LTFGDFDEHEVDALASGITFGDFDD
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCHHHHHHHHHCCCCCCCCC

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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)	46.5804	2.27563	14.1358	106
cluster_2.pdb ( medoid)	29.3397	4.90803	14.1523	144
cluster_3.pdb ( medoid)	28.2148	2.5873	13.5193	73
cluster_4.pdb ( medoid)	26.2202	6.02589	18.6394	158
cluster_5.pdb ( medoid)	22.9073	8.16334	22.7757	187
cluster_6.pdb ( medoid)	18.7569	6.39764	20.1111	120
cluster_7.pdb ( medoid)	12.1824	6.15641	16.0385	75
cluster_8.pdb ( medoid)	6.17603	11.4961	25.2289	71
cluster_9.pdb ( medoid)	4.70905	5.52128	8.59215	26
cluster_10.pdb ( medoid)	3.25542	12.2872	26.8262	40