CABS-dock: antiviral docking

Project name: antiviral docking

Status: done

submitted: 2026-05-08 10:40:36, status changed: 2026-05-08 17:40:45

Project settings

Protein sequence(s)	SIGLALLLLLLALLFWLYIVMSNWTGGALLVLYSFALMLIIIILIIFIFRRDLLCPLGGLGLLLLMITLLLIALWNLHGQALYLGIVLFIFGCLLVLGLWIYFLEILWRLGATIWQLLAFILAFFLAIILLIIALYLQQNWWTLLVDLLWLLLFMAILIWMSIGLALLLLLLALLFWLYIVMSNWTGGALLVLYSFALMLIIIILIIFIFRRDLLCPLGGLGLLLLMITLLLIALWNLHGQALYLGIVLFIFGCLLVLGLWIYFLEILWRLGATIWQLLAFILAFFLAIILLIIALYLQQNWWTLLVDLLWLLLFMAILIWM input pdb
Peptide sequence	VCYFMVFLQYGRKKRRQRR
Simulation mc cycles	50
Peptide secondary structure psipred	CCHHHHHHHHHHHHHHCCC

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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

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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)	60.3064	1.75769	5.07351	106
cluster_2.pdb ( medoid)	29.7145	4.37497	9.14989	130
cluster_3.pdb ( medoid)	26.2286	4.23202	10.2831	111
cluster_4.pdb ( medoid)	25.8575	4.56347	14.5807	118
cluster_5.pdb ( medoid)	20.3848	4.31695	11.6083	88
cluster_6.pdb ( medoid)	14.9319	6.02737	12.6524	90
cluster_7.pdb ( medoid)	14.5496	6.04827	13.9619	88
cluster_8.pdb ( medoid)	13.2776	10.9206	25.7677	145
cluster_9.pdb ( medoid)	9.68567	7.12393	13.9916	69
cluster_10.pdb ( medoid)	8.36234	6.5771	19.7827	55