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Status: Done started: 2020-Apr-15 19:44:43 UTC
Project NameAVP1999
SequenceGLMDTVKNVAKNLAGHMLDKLKCKITGC
Secondary structure

CHHHHHHHHHHHHHHHHHHHHHHHHCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-16 01:43 UTC

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

Cluster #123456789
Cluster density89.853.934.626.920.710.910.26.22.1
Cluster size94716043331824125
Average cluster RMSD1.01.31.71.61.61.62.31.92.4

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 1.39 1.22 1.29 0.73 1.23 3.30 1.32 4.79
2 1.39 0.00 1.64 1.91 1.50 2.05 3.62 1.98 4.61
3 1.22 1.64 0.00 1.70 1.38 1.55 2.91 1.65 4.10
4 1.29 1.91 1.70 0.00 1.43 1.18 3.35 1.66 4.78
5 0.73 1.50 1.38 1.43 0.00 1.55 3.10 1.31 4.78
6 1.23 2.05 1.55 1.18 1.55 0.00 3.52 1.69 5.04
7 3.30 3.62 2.91 3.35 3.10 3.52 0.00 3.12 4.02
8 1.32 1.98 1.65 1.66 1.31 1.69 3.12 0.00 4.67
9 4.79 4.61 4.10 4.78 4.78 5.04 4.02 4.67 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 0.97 0.95 0.94 0.97 0.95 0.71 0.95 0.69
2 0.97 1.00 0.94 0.94 0.95 0.94 0.73 0.93 0.69
3 0.95 0.94 1.00 0.91 0.93 0.91 0.73 0.93 0.70
4 0.94 0.94 0.91 1.00 0.95 0.95 0.74 0.91 0.67
5 0.97 0.95 0.93 0.95 1.00 0.95 0.73 0.95 0.69
6 0.95 0.94 0.91 0.95 0.95 1.00 0.72 0.90 0.69
7 0.71 0.73 0.73 0.74 0.73 0.72 1.00 0.75 0.63
8 0.95 0.93 0.93 0.91 0.95 0.90 0.75 1.00 0.69
9 0.69 0.69 0.70 0.67 0.69 0.69 0.63 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.


 

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