Project name: 6b5m_nvdp_exp

Status: done

submitted: 2018-10-09 13:48:14, status changed: 2018-10-10 02:22:18

Project settings
Protein sequence(s) VQLVQSGAEVKKPGASVKVSCKASGYTFTSYAIHWVRQAPGQRLEWMGWIKAGNGNTRYSQKFQDRVTITRDTSTTTAYMELSSLRSEDTAVYYCALLTVLTPDDAFDIWGQGTMVTVSSDIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPNLLIYWASTRQSGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCHQYYSSPLTFGGGTKVEIK input pdb
Peptide sequence NVDPNANPNVDPNANPNVDP
Simulation mc cycles100
Peptide secondary structure psipred CCCCCCCCCCCCCCCCCCCC
Flexible regions
105:L - 95:L 109:H - 96:H
Unlikely to bind regions
62:L - 93:L 41:L - 51:L 26:L - 3:L 62:H - 92:H 39:H - 44:H
25:H - 3:H 112:H - 120:H
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) 41.8462 1.98345 7.06917 83
cluster_2.pdb ( medoid) 25.2047 7.10186 34.9426 179
cluster_3.pdb ( medoid) 23.4015 6.32437 24.3184 148
cluster_4.pdb ( medoid) 18.0749 8.68609 44.6168 157
cluster_5.pdb ( medoid) 5.84055 10.7866 21.1282 63
cluster_6.pdb ( medoid) 5.67135 12.1664 35.4273 69
cluster_7.pdb ( medoid) 4.32029 21.0634 66.1865 91
cluster_8.pdb ( medoid) 3.22249 25.4461 62.2451 82
cluster_9.pdb ( medoid) 3.02119 25.1557 70.1944 76
cluster_10.pdb ( medoid) 2.38858 14.6531 61.5572 35

 
Laboratory of Theory of Biopolymers 2015