Project name: NDM + Ib-AMP3

Status: done

submitted: 2018-01-02 09:48:43, status changed: 2018-01-02 18:17:32

Project settings
Protein sequence(s) MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR input pdb
Peptide sequence QYRHRCCAWGPGRKYCKRWC
Simulation mc cycles50
Peptide secondary structure psipred CCCCCEECCCCCCHHHHHCC
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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) 70.8822 1.39668 5.40113 99
cluster_2.pdb ( medoid) 20.1223 10.9331 30.8779 220
cluster_3.pdb ( medoid) 17.9536 6.62821 29.6056 119
cluster_4.pdb ( medoid) 12.6588 5.92473 26.2237 75
cluster_5.pdb ( medoid) 11.5998 10.5174 35.9722 122
cluster_6.pdb ( medoid) 9.64087 8.71291 23.2605 84
cluster_7.pdb ( medoid) 9.44635 13.6561 39.6452 129
cluster_8.pdb ( medoid) 6.0622 7.42305 36.3085 45
cluster_9.pdb ( medoid) 4.99161 13.6229 41.8425 68
cluster_10.pdb ( medoid) 2.94544 13.2408 41.9721 39

 
Laboratory of Theory of Biopolymers 2015