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Status: Done started: 2014-Mar-05 05:41:28 UTC
Project Namesufi
Secondary structure


Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2014-Mar-05 18:36 UTC

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

Cluster #1234
Cluster density10.
Cluster size1741353516
Average cluster RMSD15.915.014.721.1

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.

1 0.00 30.20 62.50 3.37
2 30.20 0.00 0.37 6.66
3 62.50 0.37 0.00 20.20
4 3.37 6.66 20.20 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.

1 1.00 0.05 0.04 0.04
2 0.05 1.00 0.05 0.05
3 0.04 0.05 1.00 0.16
4 0.04 0.05 0.16 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