CABS-dock: M4DN3

Project name: M4DN3_UPPS

Status: done

submitted: 2026-06-10 06:00:17, status changed: 2026-06-10 09:39:23

Project settings

Protein sequence(s)	KLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE input pdb
Peptide sequence	GPPG
Simulation mc cycles	50
Peptide secondary structure psipred	CCCC

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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)	102.617	1.38378	4.66733	142
cluster_2.pdb ( medoid)	81.7785	2.18884	21.4317	179
cluster_3.pdb ( medoid)	27.4632	5.35262	33.2794	147
cluster_4.pdb ( medoid)	22.9045	6.76722	33.219	155
cluster_5.pdb ( medoid)	9.02682	5.09592	19.6641	46
cluster_6.pdb ( medoid)	7.84936	11.4659	36.4951	90
cluster_7.pdb ( medoid)	7.05652	10.9119	29.4493	77
cluster_8.pdb ( medoid)	6.80958	12.923	35.928	88
cluster_9.pdb ( medoid)	2.66394	14.2646	37.5414	38
cluster_10.pdb ( medoid)	2.39264	15.882	31.2278	38