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Status: Done started: 2019-Dec-12 00:46:01 UTC
Project Name1bwx
SequenceSVSEIQLMHNLGKHLNSMERVEWLRKKLQDVHNFVALGA
Secondary structure

CCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2019-Dec-12 06:50 UTC

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

Cluster #12345678
Cluster density50.624.012.19.75.74.83.00.6
Cluster size1276953482621142
Average cluster RMSD2.52.94.44.94.54.44.73.3

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 12.80 11.30 13.20 4.03 6.05 5.86 5.73
2 12.80 0.00 3.63 4.47 12.30 9.38 10.40 15.20
3 11.30 3.63 0.00 5.98 11.00 7.72 9.54 13.60
4 13.20 4.47 5.98 0.00 12.50 9.69 10.20 15.10
5 4.03 12.30 11.00 12.50 0.00 7.22 4.21 5.80
6 6.05 9.38 7.72 9.69 7.22 0.00 7.06 9.20
7 5.86 10.40 9.54 10.20 4.21 7.06 0.00 7.13
8 5.73 15.20 13.60 15.10 5.80 9.20 7.13 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 0.58 0.53 0.46 0.69 0.67 0.66 0.56
2 0.58 1.00 0.66 0.59 0.53 0.54 0.46 0.52
3 0.53 0.66 1.00 0.60 0.50 0.51 0.44 0.51
4 0.46 0.59 0.60 1.00 0.49 0.47 0.52 0.47
5 0.69 0.53 0.50 0.49 1.00 0.58 0.70 0.60
6 0.67 0.54 0.51 0.47 0.58 1.00 0.52 0.53
7 0.66 0.46 0.44 0.52 0.70 0.52 1.00 0.47
8 0.56 0.52 0.51 0.47 0.60 0.53 0.47 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