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Status: Done started: 2015-Nov-14 21:54:27 UTC
Project NamePOLYALANINE
SequenceAAAAA
Secondary structure

CCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Nov-15 00:57 UTC

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

Cluster #12345678
Cluster density112.373.469.758.342.937.827.48.1
Cluster size845970503535198
Average cluster RMSD0.70.81.00.90.80.90.71.0

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 1.78 1.45 3.04 0.37 0.50 1.23 1.72
2 1.78 0.00 0.46 2.60 1.92 1.75 1.83 1.93
3 1.45 0.46 0.00 2.77 1.55 1.48 1.51 1.83
4 3.04 2.60 2.77 0.00 3.07 3.00 2.81 1.87
5 0.37 1.92 1.55 3.07 0.00 0.54 1.13 1.79
6 0.50 1.75 1.48 3.00 0.54 0.00 1.45 1.86
7 1.23 1.83 1.51 2.81 1.13 1.45 0.00 1.14
8 1.72 1.93 1.83 1.87 1.79 1.86 1.14 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 0.85 0.85 0.55 1.00 1.00 0.85 0.70
2 0.85 1.00 1.00 0.50 0.85 0.85 0.65 0.60
3 0.85 1.00 1.00 0.50 0.85 0.85 0.80 0.75
4 0.55 0.50 0.50 1.00 0.55 0.55 0.65 0.85
5 1.00 0.85 0.85 0.55 1.00 1.00 0.90 0.70
6 1.00 0.85 0.85 0.55 1.00 1.00 0.75 0.65
7 0.85 0.65 0.80 0.65 0.90 0.75 1.00 0.95
8 0.70 0.60 0.75 0.85 0.70 0.65 0.95 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