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Status: Done started: 2018-Mar-29 06:10:34 UTC
Project NamepolyM
SequenceMMMMMMMMMMMMMMMMMMMM
Secondary structure

CHHHHHHHHHHHHHHHHHHC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Mar-29 11:22 UTC

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

Cluster #123456789
Cluster density99.997.283.154.424.219.411.69.56.0
Cluster size78806359242015147
Average cluster RMSD0.80.80.81.11.01.01.31.51.2

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.

#123456789
1 0.00 0.38 0.40 0.43 0.82 1.58 1.22 1.49 0.91
2 0.38 0.00 0.36 0.37 0.59 1.52 1.29 1.51 0.99
3 0.40 0.36 0.00 0.54 0.58 1.57 1.34 1.61 0.77
4 0.43 0.37 0.54 0.00 0.83 1.57 1.24 1.53 1.17
5 0.82 0.59 0.58 0.83 0.00 1.49 1.44 1.74 1.00
6 1.58 1.52 1.57 1.57 1.49 0.00 2.09 1.05 1.49
7 1.22 1.29 1.34 1.24 1.44 2.09 0.00 1.93 1.75
8 1.49 1.51 1.61 1.53 1.74 1.05 1.93 0.00 1.55
9 0.91 0.99 0.77 1.17 1.00 1.49 1.75 1.55 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.

#123456789
1 1.00 1.00 1.00 0.99 0.97 0.96 0.95 0.95 0.95
2 1.00 1.00 0.99 0.99 0.99 0.95 0.95 0.95 0.95
3 1.00 0.99 1.00 0.97 0.97 0.96 0.95 0.94 0.97
4 0.99 0.99 0.97 1.00 0.96 0.95 0.96 0.96 0.94
5 0.97 0.99 0.97 0.96 1.00 0.96 0.93 0.95 0.94
6 0.96 0.95 0.96 0.95 0.96 1.00 0.90 0.95 0.95
7 0.95 0.95 0.95 0.96 0.93 0.90 1.00 0.91 0.91
8 0.95 0.95 0.94 0.96 0.95 0.95 0.91 1.00 0.91
9 0.95 0.95 0.97 0.94 0.94 0.95 0.91 0.91 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