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Status: Done started: 2016-Apr-25 16:14:46 UTC
Project NameCB1
SequenceQATRSETPVEVLAQQTHG
Secondary structure

CCCCCCCHHHHHHHHHHC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Apr-25 20:54 UTC

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

Cluster #123456789
Cluster density126.119.715.612.411.29.87.57.46.6
Cluster size1375138292928171615
Average cluster RMSD1.12.62.42.32.62.82.32.22.3

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 2.82 2.75 4.57 2.12 4.01 3.39 2.88 5.22
2 2.82 0.00 2.94 3.84 3.54 3.85 3.03 2.85 4.51
3 2.75 2.94 0.00 4.81 2.89 4.25 2.40 2.22 5.83
4 4.57 3.84 4.81 0.00 4.73 3.39 5.04 4.86 2.51
5 2.12 3.54 2.89 4.73 0.00 3.54 3.30 2.88 5.54
6 4.01 3.85 4.25 3.39 3.54 0.00 4.88 4.49 3.86
7 3.39 3.03 2.40 5.04 3.30 4.88 0.00 1.55 6.05
8 2.88 2.85 2.22 4.86 2.88 4.49 1.55 0.00 5.63
9 5.22 4.51 5.83 2.51 5.54 3.86 6.05 5.63 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 0.71 0.75 0.62 0.82 0.56 0.71 0.81 0.71
2 0.71 1.00 0.74 0.61 0.68 0.58 0.69 0.71 0.61
3 0.75 0.74 1.00 0.60 0.71 0.62 0.72 0.76 0.60
4 0.62 0.61 0.60 1.00 0.60 0.57 0.58 0.61 0.76
5 0.82 0.68 0.71 0.60 1.00 0.61 0.72 0.78 0.62
6 0.56 0.58 0.62 0.57 0.61 1.00 0.56 0.56 0.54
7 0.71 0.69 0.72 0.58 0.72 0.56 1.00 0.89 0.65
8 0.81 0.71 0.76 0.61 0.78 0.56 0.89 1.00 0.69
9 0.71 0.61 0.60 0.76 0.62 0.54 0.65 0.69 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