CABS-dock: peptide

Project name: peptide_3

Status: done

submitted: 2024-07-15 08:33:39, status changed: 2024-07-15 23:35:29

Project settings

Protein sequence(s)

GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEMIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM input pdb

Peptide sequence

TNGTKRFDN

Simulation mc cycles

100

Peptide secondary structure psipred

CCCCCCCCC

Contact information

84:A 9:PEP 5.0 1.0

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 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)	20.2702	3.94668	7.5887	80
cluster_2.pdb ( medoid)	18.6356	2.57572	6.75652	48
cluster_3.pdb ( medoid)	11.7459	3.83112	7.14764	45
cluster_4.pdb ( medoid)	7.42897	5.65354	11.4321	42
cluster_5.pdb ( medoid)	6.88541	4.93798	8.73451	34
cluster_6.pdb ( medoid)	4.93489	10.5372	20.5351	52
cluster_7.pdb ( medoid)	4.82321	10.7812	25.6286	52
cluster_8.pdb ( medoid)	4.68782	3.83974	7.44524	18
cluster_9.pdb ( medoid)	3.26321	8.88696	18.3969	29
cluster_10.pdb ( medoid)	1.99035	8.0388	14.1829	16