CABS-dock: AF_PMA1

Project name: AF_PMA1_LLeuAla

Status: done

submitted: 2026-02-13 13:43:29, status changed: 2026-02-14 18:46:46

Project settings

Protein sequence(s)	LASSEIETRRKKGGWNELTTEKTNFFVQFIGYFRGPILYVMELAVLLAAGLRDWIDLGVICGILLLNAVVGWYQEKQAADVVASLKGDIAMKAVVIRDGQEQEILARELVTGDIIVVEEGTVIPADIRLICDYDKPEMSLIAVDQSAITGESLAVDKYMADTCYYTTGCKRGKAYAIVTATAKQSFVGKTAALVQGAKDQGHFKAVMDNIGTTLLVLVMFWILAAWIGGFYRHLKIATPEHEDNNLLHYTLILLIIGVPVGLPVVTTTTLAVGAAYLAEQKAIVQKLTAIESLAGVDILCSDKTGTLTREDTAHTIAEAQHLGLSVKMLTGDALAIAKETCKMLALSTKVYDSERLIHGGLAGSAQHDLVEKADGFAEVFPEHKYQVVEMLQQRGHLTAMTGDGVNDAPSLKKADCGIAVEGSTEAAQAAADIVFLAPGLSTIVDAIKLARQIFQRMKAYIQYRIALCLHLEIYLVTSMIIIDETLNSELVVFIALFADLATIAVAYDNAHYEMRPVEWQLPKIWVISIVLGVLLAGATWIMRASLFLNDGGLIQNFGSPQEMIFLEVALTENWLIFVTRGGKTWPSWQLVGAIFVVDVLATLFCVFGWLSGDYRQTSPPSHAEFSVNGDVDIVTVVVIWGYSIGVTIIIAVVYYILTIIPALDNLGRKTRSKADTKIENMIAHLSKLA input pdb
Peptide sequence	ALGRKKFWFW
Simulation mc cycles	50
Peptide secondary structure psipred	CCCCCCCCCC

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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

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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)	31.2618	6.81343	16.5279	213
cluster_2.pdb ( medoid)	24.396	4.46794	9.33196	109
cluster_3.pdb ( medoid)	22.7319	4.66306	11.512	106
cluster_4.pdb ( medoid)	17.8163	8.41926	54.8155	150
cluster_5.pdb ( medoid)	16.001	7.56205	51.8172	121
cluster_6.pdb ( medoid)	14.9823	4.47195	13.2087	67
cluster_7.pdb ( medoid)	8.10094	10.1223	39.0137	82
cluster_8.pdb ( medoid)	5.85231	7.51841	33.1399	44
cluster_9.pdb ( medoid)	4.44515	12.823	38.6663	57
cluster_10.pdb ( medoid)	2.50157	20.3872	61.5173	51