CABS-dock: USP7 peptide

Project name: USP7 peptide

Status: done

submitted: 2025-11-25 06:37:52, status changed: 2025-11-26 11:56:26

Project settings

Protein sequence(s)	MSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDDNVENKMKGTCVEGTIPKLFRGKMMVSYIQCKEVDYRSDRRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEEAIEHNYGGHDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEEKRIEAQKRKERQEHHMSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESSFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEA input pdb
Peptide sequence	SGPRGPRKCARKTRHAETSGA
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCCCCCHHCCHHCCCC

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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)	49.645	2.07473	17.8342	103
cluster_2.pdb ( medoid)	19.7322	5.11853	22.2395	101
cluster_3.pdb ( medoid)	17.1131	5.84346	21.1998	100
cluster_4.pdb ( medoid)	14.7397	6.85223	21.7175	101
cluster_5.pdb ( medoid)	12.7826	12.517	28.7269	160
cluster_6.pdb ( medoid)	10.7009	9.53192	31.4951	102
cluster_7.pdb ( medoid)	8.04323	16.5356	40.5424	133
cluster_8.pdb ( medoid)	6.42777	8.7122	21.1895	56
cluster_9.pdb ( medoid)	6.38123	13.6337	28.2851	87
cluster_10.pdb ( medoid)	4.07306	13.9944	29.8352	57