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Status: Done started: 2017-Aug-29 22:01:12 UTC
Project NameDHRS3_TMD2
SequenceLSRENVLITGGGRGIGRQLAR
Secondary structure

CCCCEEEEECCCCHHHHHHHC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Aug-30 02:54 UTC

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

Cluster #12345678
Cluster density52.718.115.112.210.710.05.74.0
Cluster size12956414033321712
Average cluster RMSD2.43.12.73.33.13.23.03.0

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 3.82 2.87 5.48 5.02 6.67 8.85 7.27
2 3.82 0.00 3.82 4.44 3.20 5.82 6.73 6.26
3 2.87 3.82 0.00 4.06 4.24 5.36 7.23 5.59
4 5.48 4.44 4.06 0.00 4.00 4.66 4.94 4.55
5 5.02 3.20 4.24 4.00 0.00 5.33 5.68 5.95
6 6.67 5.82 5.36 4.66 5.33 0.00 4.77 4.02
7 8.85 6.73 7.23 4.94 5.68 4.77 0.00 4.33
8 7.27 6.26 5.59 4.55 5.95 4.02 4.33 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 0.79 0.74 0.54 0.63 0.58 0.52 0.48
2 0.79 1.00 0.68 0.58 0.73 0.59 0.56 0.50
3 0.74 0.68 1.00 0.63 0.64 0.63 0.54 0.55
4 0.54 0.58 0.63 1.00 0.62 0.55 0.57 0.58
5 0.63 0.73 0.64 0.62 1.00 0.57 0.56 0.49
6 0.58 0.59 0.63 0.55 0.57 1.00 0.56 0.59
7 0.52 0.56 0.54 0.57 0.56 0.56 1.00 0.58
8 0.48 0.50 0.55 0.58 0.49 0.59 0.58 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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