CABS-dock: braf_dimer_peptide

Project name: braf_dimer_peptide_9

Status: done

submitted: 2025-12-28 09:42:18, status changed: 2025-12-29 04:10:51

Project settings

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

Re-submit project

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

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)	48.2073	3.00784	5.86238	145
cluster_2.pdb ( medoid)	20.6853	5.55951	36.1555	115
cluster_3.pdb ( medoid)	16.9978	6.53025	41.493	111
cluster_4.pdb ( medoid)	14.4131	10.8235	32.3077	156
cluster_5.pdb ( medoid)	13.7324	10.8503	43.7613	149
cluster_6.pdb ( medoid)	12.3222	4.78809	21.6017	59
cluster_7.pdb ( medoid)	10.7107	12.5109	48.0742	134
cluster_8.pdb ( medoid)	2.93286	21.4807	45.257	63
cluster_9.pdb ( medoid)	2.20674	19.4858	44.946	43
cluster_10.pdb ( medoid)	1.21694	20.5433	55.0869	25