CABS-dock: MARCKS-NMT2

Project name: MARCKS-NMT2

Status: done

submitted: 2025-12-31 08:40:22, status changed: 2025-12-31 15:59:43

Project settings

Protein sequence(s)	GFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGIVLQ input pdb
Peptide sequence	MGSQSSKAPRGDVTAEEAAG
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCCCCCCCCHHHHCC

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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)	14.9003	11.9461	28.5253	178
cluster_2.pdb ( medoid)	12.5448	11.7978	29.9172	148
cluster_3.pdb ( medoid)	11.3513	9.07388	41.0991	103
cluster_4.pdb ( medoid)	10.2582	11.3081	41.0136	116
cluster_5.pdb ( medoid)	9.15463	11.9065	27.9993	109
cluster_6.pdb ( medoid)	7.50428	15.7244	44.7505	118
cluster_7.pdb ( medoid)	6.93528	7.20952	17.5201	50
cluster_8.pdb ( medoid)	6.5386	14.2232	39.3777	93
cluster_9.pdb ( medoid)	4.56874	11.8195	30.8467	54
cluster_10.pdb ( medoid)	2.53135	12.2464	26.2487	31