Project name: 6d01_nvdp_exp

Status: done

submitted: 2018-10-09 13:08:54, status changed: 2018-10-10 02:13:48

Project settings
Protein sequence(s) QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGMHWVRQAPGKGLEWVAVIWYDGSKKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARVRDSSDYYGDAFDIWGQGTMVTVSDIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASNLESGVPLRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNNYWTFGQGTKVEIK input pdb
Peptide sequence NVDPNANPNVDPNANPNVDP
Simulation mc cycles100
Peptide secondary structure psipred CCCCCCCCCCCCCCCCCCCC
Flexible regions
89:B - 99:B 112:A - 98:A
Unlikely to bind regions
106:B - 98:B 45:B - 87:B 26:B - 44:B 1:B - 25:B 94:A - 96:A
63:A - 93:A 1:A - 24:A
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 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) 29.342 3.51033 37.5713 103
cluster_2.pdb ( medoid) 18.7316 6.29953 23.3735 118
cluster_3.pdb ( medoid) 17.9521 7.52003 30.9262 135
cluster_4.pdb ( medoid) 16.6856 6.71237 39.4049 112
cluster_5.pdb ( medoid) 15.1643 9.10033 37.0185 138
cluster_6.pdb ( medoid) 6.79554 14.4212 45.3906 98
cluster_7.pdb ( medoid) 5.00088 17.7969 45.9049 89
cluster_8.pdb ( medoid) 4.84982 16.2893 48.0586 79
cluster_9.pdb ( medoid) 4.29481 17.9286 37.2851 77
cluster_10.pdb ( medoid) 2.43832 20.916 38.0157 51

 
Laboratory of Theory of Biopolymers 2015