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Status: Done started: 2014-Jul-17 15:42:01 UTC
Project Nameexpe3
SequenceAGHTLFQDVFRRADKNDDGKLSFEEFQNYFADGVLSLGELQELFSGIDGHLTDNLETEKLCDYFSEHLGVYRPVLAALES
Secondary structure

CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHCC

Simulation (CABS) temperature2.5 - 1.0
Estimated finish time2014-Jul-18 04:27 UTC

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

Cluster #12345678
Cluster density50.329.526.224.520.819.312.09.6
Cluster size9555494635391823
Average cluster RMSD1.91.91.91.91.72.01.52.4

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 3.52 7.27 3.82 1.44 1.29 5.24 5.84
2 3.52 0.00 5.83 1.56 3.90 3.87 2.99 4.46
3 7.27 5.83 0.00 5.10 7.17 7.72 3.93 3.27
4 3.82 1.56 5.10 0.00 4.09 4.19 2.18 3.60
5 1.44 3.90 7.17 4.09 0.00 1.64 5.38 5.89
6 1.29 3.87 7.72 4.19 1.64 0.00 5.68 6.28
7 5.24 2.99 3.93 2.18 5.38 5.68 0.00 2.83
8 5.84 4.46 3.27 3.60 5.89 6.28 2.83 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 0.68 0.57 0.69 0.89 0.87 0.58 0.67
2 0.68 1.00 0.59 0.84 0.63 0.63 0.73 0.71
3 0.57 0.59 1.00 0.61 0.56 0.56 0.62 0.67
4 0.69 0.84 0.61 1.00 0.64 0.65 0.80 0.80
5 0.89 0.63 0.56 0.64 1.00 0.86 0.54 0.66
6 0.87 0.63 0.56 0.65 0.86 1.00 0.56 0.67
7 0.58 0.73 0.62 0.80 0.54 0.56 1.00 0.75
8 0.67 0.71 0.67 0.80 0.66 0.67 0.75 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.


 

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