Project name: PDL1-PEPTIDE_DOCKING

Status: done

submitted: 2018-01-10 23:40:37, status changed: 2018-01-11 04:10:48

Project settings
Protein sequence(s) AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNA input pdb
Peptide sequence GSGSGSTYLCGAISLAPKAQIKESL
Simulation mc cycles50
Peptide secondary structure psipred CCCCCCHHHHHHHHCCCHHHHHHCC
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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
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 residuePeptide residue
Receptor residuePeptide residue
Receptor residuePeptide 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 namecluster density average rmsdmax rmsdnumber of elements
cluster_1.pdb ( medoid) 24.418 4.54582 24.4415 111
cluster_2.pdb ( medoid) 19.6248 3.61788 15.9114 71
cluster_3.pdb ( medoid) 15.9537 5.13986 21.6595 82
cluster_4.pdb ( medoid) 15.8432 7.44801 23.3515 118
cluster_5.pdb ( medoid) 13.2392 7.7044 23.024 102
cluster_6.pdb ( medoid) 11.349 10.3974 29.2005 118
cluster_7.pdb ( medoid) 9.97559 5.91444 20.4154 59
cluster_8.pdb ( medoid) 9.36632 11.9577 25.6208 112
cluster_9.pdb ( medoid) 9.09336 7.14807 31.2538 65
cluster_10.pdb ( medoid) 5.68979 10.8967 24.0331 62

 
Laboratory of Theory of Biopolymers 2015