CABS-dock: Example project

Project name: Example project

Status: done

submitted: 2021-04-13 17:53:02, status changed: 2024-09-03 12:26:44

Project settings

Protein sequence(s)	MAPGGYVAPKAVWLPAVKAKGLEISSGTFTHRQGHIYMEEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVVSQYIYQVYDSILKNGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDDIPNENELQFQIKECHLNADTVSSSKLQNNNVYTIAKRNVEGQDMLLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN input pdb
Peptide sequence	SFGDGFADF
Simulation mc cycles	50
Peptide secondary structure	CCCCHHHHC

Re-submit project

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)	32.629	3.8003	14.5889	124
cluster_2.pdb ( medoid)	22.3522	6.48705	24.8381	145
cluster_3.pdb ( medoid)	16.3423	7.28172	16.3855	119
cluster_4.pdb ( medoid)	10.2769	12.9416	58.302	133
cluster_5.pdb ( medoid)	8.2614	9.80464	25.6801	81
cluster_6.pdb ( medoid)	7.96169	6.78248	13.6178	54
cluster_7.pdb ( medoid)	7.32451	11.6049	50.9502	85
cluster_8.pdb ( medoid)	7.1166	10.8198	32.7433	77
cluster_9.pdb ( medoid)	1.30644	17.605	35.4707	23
cluster_10.pdb ( medoid)	1.16716	17.1356	43.8347	20