CABS-dock: VRMALF

Project name: VRMALF

Status: done

submitted: 2026-02-17 15:03:07, status changed: 2026-02-18 03:54:27

Project settings

Protein sequence(s)	EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFRPRFLELLKSECHFFNGTERVRFLERYFHNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGQVDNYCRHNYGVVESFTVQRRVHPQVTVYPAKHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA input pdb
Peptide sequence	VRMALF
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCC

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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)	56.8111	1.83063	20.7254	104
cluster_2.pdb ( medoid)	47.9656	2.62688	11.8787	126
cluster_3.pdb ( medoid)	43.8287	3.71902	12.7825	163
cluster_4.pdb ( medoid)	31.4074	3.43868	8.19972	108
cluster_5.pdb ( medoid)	24.6344	2.59799	22.0617	64
cluster_6.pdb ( medoid)	17.4338	9.92327	34.1243	173
cluster_7.pdb ( medoid)	13.4244	5.9593	21.109	80
cluster_8.pdb ( medoid)	10.5707	8.4195	22.571	89
cluster_9.pdb ( medoid)	10.5263	5.70001	24.5817	60
cluster_10.pdb ( medoid)	6.53918	5.04651	20.4942	33