CABS-dock: braf_dimer_peptide

Project name: braf_dimer_peptide_7

Status: done

submitted: 2025-12-28 09:40:52, status changed: 2025-12-29 03:57:57

Project settings

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

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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)	42.9202	2.5163	24.1246	108
cluster_2.pdb ( medoid)	19.6893	5.63758	24.9012	111
cluster_3.pdb ( medoid)	18.4858	6.0587	45.6773	112
cluster_4.pdb ( medoid)	17.6044	3.80586	14.7951	67
cluster_5.pdb ( medoid)	16.664	6.12099	18.2315	102
cluster_6.pdb ( medoid)	13.7063	10.2872	48.2304	141
cluster_7.pdb ( medoid)	12.306	9.91389	27.9373	122
cluster_8.pdb ( medoid)	11.1416	10.2319	38.902	114
cluster_9.pdb ( medoid)	7.93042	12.1053	43.9252	96
cluster_10.pdb ( medoid)	1.55404	17.3741	48.2896	27