CABS-dock: braf_dimer_peptide

Project name: braf_dimer_peptide_10

Status: done

submitted: 2025-12-28 09:42:58, status changed: 2025-12-29 04:28:08

Project settings

Protein sequence(s)	DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYKHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRRDLKSNNIFLHEDNNTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAEECLKKKRDERPSFPRILAEIEELAREDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYKHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRRDLKSNNIFLHEDNNTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAEECLKKKRDERPSFPRILAEIEELARE input pdb
Peptide sequence	LRKTRHVNILLFMG
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCEEEEEEECC

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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 3Dmol (WebGL)

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)	51.1652	2.13035	8.85709	109
cluster_2.pdb ( medoid)	36.0551	2.77354	5.35518	100
cluster_3.pdb ( medoid)	31.3134	5.49286	15.091	172
cluster_4.pdb ( medoid)	29.1175	6.97175	23.3968	203
cluster_5.pdb ( medoid)	17.8755	3.13277	6.13815	56
cluster_6.pdb ( medoid)	13.9886	5.29004	18.747	74
cluster_7.pdb ( medoid)	13.6061	8.37857	31.7151	114
cluster_8.pdb ( medoid)	7.40276	6.48407	30.6335	48
cluster_9.pdb ( medoid)	6.63281	11.1567	23.7144	74
cluster_10.pdb ( medoid)	3.98905	12.5343	27.2597	50