CABS-dock: APB database

Project name: APB database

Status: done

submitted: 2026-01-10 11:15:01, status changed: 2026-01-10 15:52:07

Project settings

Protein sequence(s)	MSRIILFAAILAIIAVSANGASNLPALDMASIPDEYKDLVPPEVTTFYNELTEDDKKILKEVAEKHSEYATDEDALNALKEKSEKLYTKANELRNLVKDRISKLNPEAKTFVDTIIEKLKALRPKEDEKPNLTELRKEANEIVEKFKALSEEAKESLKTNFPKITGVIQNEKFQKLAQSLLKPEGAAAPA input pdb
Peptide sequence	AKKVFKRLEKLFSKIQNDK
Simulation mc cycles	50
Peptide secondary structure psipred	CHHHHHHHHHHHHHHHHCC

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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)	21.8023	6.32962	25.3931	138
cluster_2.pdb ( medoid)	19.8783	7.69684	34.5013	153
cluster_3.pdb ( medoid)	17.4847	5.26174	21.3094	92
cluster_4.pdb ( medoid)	15.4972	8.38861	32.9654	130
cluster_5.pdb ( medoid)	12.9587	7.4853	34.5663	97
cluster_6.pdb ( medoid)	12.9325	14.7689	30.5344	191
cluster_7.pdb ( medoid)	7.70923	6.87487	31.8611	53
cluster_8.pdb ( medoid)	6.95004	11.9424	28.1077	83
cluster_9.pdb ( medoid)	3.93802	8.88771	19.6778	35
cluster_10.pdb ( medoid)	2.37855	11.7719	23.7676	28