CABS-dock: LPS Vaccine

Project name: LPS Vaccine

Status: done

submitted: 2025-04-26 14:38:40, status changed: 2025-04-27 19:25:26

Project settings

Protein sequence(s)	SHSMRYFYTAVSEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQADRVSLRNLRGYYNQSEAGSHTLQWMYGCDLPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQWRAYLEGTCVEWLRRYLENGKETLQRAEHPKTHVTHHPVSTLRCWALGFYPAEITLTWQRDQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSGDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSGDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQADRVSLRNLRGYYNQSEAGSHTLQWMYGCDLGPGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQWRAYLEGTCVEWLRRYLENGKETLQRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW input pdb
Peptide sequence	LSSAVTASI
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCCC

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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 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

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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)	86.7612	1.68278	4.9284	146
cluster_2.pdb ( medoid)	46.0382	3.32332	9.61492	153
cluster_3.pdb ( medoid)	44.7528	2.25684	5.16475	101
cluster_4.pdb ( medoid)	21.8019	4.63261	17.1002	101
cluster_5.pdb ( medoid)	21.2996	2.77001	7.84001	59
cluster_6.pdb ( medoid)	18.1036	3.47997	8.21218	63
cluster_7.pdb ( medoid)	17.4694	4.40771	9.70778	77
cluster_8.pdb ( medoid)	16.5615	2.8379	7.81323	47
cluster_9.pdb ( medoid)	16.4095	3.22983	9.01998	53
cluster_10.pdb ( medoid)	10.4632	13.8581	36.3138	145