CABS-dock: RecA-Scrambled

Project name: RecA-Scrambled

Status: done

submitted: 2026-01-11 18:24:32, status changed: 2026-01-12 03:24:11

Project settings

Protein sequence(s)	DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGLAARMMSQAMRKLAGNLKQSNTLLIFINQTGGNALKFYASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL input pdb
Peptide sequence	QKAIHVKQAILGKHVNE
Simulation mc cycles	50
Peptide secondary structure psipred	CCCHHHHHHHHHCCCCC

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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)	31.8576	5.61875	18.1347	179
cluster_2.pdb ( medoid)	23.0944	5.67236	22.8627	131
cluster_3.pdb ( medoid)	18.5887	11.889	30.6989	221
cluster_4.pdb ( medoid)	17.8559	2.7442	14.3556	49
cluster_5.pdb ( medoid)	17.5541	6.66512	27.7977	117
cluster_6.pdb ( medoid)	16.6393	5.64928	20.8734	94
cluster_7.pdb ( medoid)	10.0321	5.68175	13.1609	57
cluster_8.pdb ( medoid)	8.92499	12.2129	27.1187	109
cluster_9.pdb ( medoid)	5.3331	4.5002	16.3844	24
cluster_10.pdb ( medoid)	1.54166	12.3244	18.8474	19