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Status: Done started: 2016-May-17 18:48:47 UTC
Project Nameiqbal2
SequencePSAAITNNRVIQPLNQRQVYNYGVSV
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2016-May-18 00:02 UTC

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

Cluster #12345678
Cluster density122.814.114.16.55.34.03.42.6
Cluster size18246443017161510
Average cluster RMSD1.53.33.14.63.24.04.43.8

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 7.24 2.77 9.11 3.61 10.00 8.23 8.14
2 7.24 0.00 6.73 3.99 7.28 5.39 4.97 4.81
3 2.77 6.73 0.00 8.35 3.84 9.50 7.46 7.85
4 9.11 3.99 8.35 0.00 8.86 4.62 4.03 6.54
5 3.61 7.28 3.84 8.86 0.00 9.55 7.50 7.97
6 10.00 5.39 9.50 4.62 9.55 0.00 5.74 5.21
7 8.23 4.97 7.46 4.03 7.50 5.74 0.00 7.69
8 8.14 4.81 7.85 6.54 7.97 5.21 7.69 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 0.59 0.74 0.44 0.58 0.43 0.46 0.38
2 0.59 1.00 0.54 0.56 0.51 0.39 0.53 0.43
3 0.74 0.54 1.00 0.43 0.57 0.43 0.43 0.38
4 0.44 0.56 0.43 1.00 0.41 0.45 0.57 0.38
5 0.58 0.51 0.57 0.41 1.00 0.38 0.42 0.41
6 0.43 0.39 0.43 0.45 0.38 1.00 0.39 0.48
7 0.46 0.53 0.43 0.57 0.42 0.39 1.00 0.34
8 0.38 0.43 0.38 0.38 0.41 0.48 0.34 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