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Status: Done started: 2014-Mar-10 20:18:12 UTC
Project Namesgk-model
SequenceVHFNIQQDCGHFLAEVPNRLLPWEDPDDPEKDEDDMEETEEDAKGETDGKNPKPCSEAASSQKENQGVMSKKQRSHVVVI TREVPCLTVADFVRDSLAQHGKSPDLYERQVCLLLLQLCSGLEHLKPYHVTHCDLRLENLLLVHYQPGGTAQGFGPAEPS PTSSYPTRLIVSNFSQAKQKSHLVDPEILRDQSRLAPEIITATQYKKCDEFQTGILIYEMLHLPNPFDENPELKEREYTR ADLPRIPFRSPYSRGLQQLASCLLNPNPSERILISDAKGILQCLLW
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE ECCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCEECHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH HCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2014-Mar-11 09:13 UTC

Provided templates.

Time evolution of structural features: CABS energy, End-to-end distance and Radius of gyration.

Cluster #12345678
Cluster density51.842.622.221.521.318.015.214.7
Cluster size7155464438393334
Average cluster RMSD1.41.32.12.01.82.22.22.3

Clustering of protein models is the task of separating a set of protein models (here a protein dynamics trajectory) into groups (called clusters). The clustering is done in such a way that models are more similar in the same group to each other (here in the sense of RMSD measure), than those in other groups (clusters). CABSfold utilizes classical K-means clustering method.
After clustering is done, each cluster representative is chosen (always the model which average dissimilarity to all models in a cluster is minimal). Predicted protein models, presented in the Predicted structures tab, are each cluster representatives (the clusters and the corresponding models are marked by the same numbers, e.g. Model 1 represents Cluster 1).
The clusters are numbered/ranked according to cluster density values, from the most dense (numbered as a first) to the least dense one.

#12345678
1 0.00 4.60 1.94 3.76 2.04 3.78 3.53 4.13
2 4.60 0.00 3.46 2.04 4.53 2.13 2.61 3.18
3 1.94 3.46 0.00 2.58 1.74 2.36 2.29 2.81
4 3.76 2.04 2.58 0.00 3.45 1.72 1.93 2.57
5 2.04 4.53 1.74 3.45 0.00 3.25 2.78 3.19
6 3.78 2.13 2.36 1.72 3.25 0.00 1.41 1.77
7 3.53 2.61 2.29 1.93 2.78 1.41 0.00 1.80
8 4.13 3.18 2.81 2.57 3.19 1.77 1.80 0.00

The table contains RMSD values (calculated on the Cα atoms) between the predicted models.
Read more about the root-mean-square deviation (RMSD) measure.

#12345678
1 1.00 0.84 0.93 0.86 0.91 0.90 0.92 0.91
2 0.84 1.00 0.88 0.83 0.84 0.90 0.87 0.87
3 0.93 0.88 1.00 0.88 0.92 0.93 0.94 0.92
4 0.86 0.83 0.88 1.00 0.87 0.88 0.87 0.84
5 0.91 0.84 0.92 0.87 1.00 0.90 0.92 0.90
6 0.90 0.90 0.93 0.88 0.90 1.00 0.93 0.91
7 0.92 0.87 0.94 0.87 0.92 0.93 1.00 0.94
8 0.91 0.87 0.92 0.84 0.90 0.91 0.94 1.00

The table contains GDT_TS values (calculated on the Cα atoms) between the predicted models.
Read more about the global distance test (GDT, also written as GDT_TS to represent "total score") measure.


 

© Laboratory of Theory of Biopolymers 2013