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Status: Done started: 2020-Apr-13 15:11:54 UTC
Project NameAVP1737
SequenceHRILMRIRQMMA
Secondary structure

CHHHHHHHHHHC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-13 19:44 UTC

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

Cluster #123456789
Cluster density130.2121.6106.282.074.936.536.016.816.1
Cluster size636154424334301518
Average cluster RMSD0.50.50.50.50.60.90.80.91.1

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.

#123456789
1 0.00 0.31 0.28 0.27 0.25 0.55 0.39 0.56 1.19
2 0.31 0.00 0.28 0.35 0.38 0.72 0.28 0.78 1.34
3 0.28 0.28 0.00 0.39 0.24 0.57 0.42 0.71 1.25
4 0.27 0.35 0.39 0.00 0.45 0.56 0.51 0.71 1.08
5 0.25 0.38 0.24 0.45 0.00 0.52 0.40 0.54 1.25
6 0.55 0.72 0.57 0.56 0.52 0.00 0.80 0.66 0.87
7 0.39 0.28 0.42 0.51 0.40 0.80 0.00 0.68 1.46
8 0.56 0.78 0.71 0.71 0.54 0.66 0.68 0.00 1.29
9 1.19 1.34 1.25 1.08 1.25 0.87 1.46 1.29 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 1.00 1.00 0.98 0.98 0.98 0.94
2 1.00 1.00 1.00 1.00 1.00 0.98 1.00 0.98 0.94
3 1.00 1.00 1.00 1.00 1.00 0.98 0.98 0.98 0.94
4 1.00 1.00 1.00 1.00 0.98 0.98 0.98 0.98 0.96
5 1.00 1.00 1.00 0.98 1.00 0.98 0.98 0.98 0.94
6 0.98 0.98 0.98 0.98 0.98 1.00 0.96 0.96 0.96
7 0.98 1.00 0.98 0.98 0.98 0.96 1.00 0.98 0.94
8 0.98 0.98 0.98 0.98 0.98 0.96 0.98 1.00 0.94
9 0.94 0.94 0.94 0.96 0.94 0.96 0.94 0.94 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