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Status: Done started: 2020-Mar-31 23:02:37 UTC
Project NameAVP1944
SequenceTDVILMCFSIDSPDSLENA
Secondary structure

CCEEEEEEEECCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-01 04:20 UTC

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

Cluster #12345678
Cluster density44.024.213.913.910.610.49.78.7
Cluster size9568414231302825
Average cluster RMSD2.22.82.93.02.92.92.92.9

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 3.97 6.32 10.70 6.36 9.43 11.90 13.30
2 3.97 0.00 5.28 8.52 4.30 7.22 9.31 11.30
3 6.32 5.28 0.00 5.28 4.12 5.56 6.99 7.69
4 10.70 8.52 5.28 0.00 5.77 4.37 3.87 4.50
5 6.36 4.30 4.12 5.77 0.00 4.32 6.41 8.38
6 9.43 7.22 5.56 4.37 4.32 0.00 4.04 6.54
7 11.90 9.31 6.99 3.87 6.41 4.04 0.00 4.64
8 13.30 11.30 7.69 4.50 8.38 6.54 4.64 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 0.54 0.56 0.50 0.50 0.51 0.49 0.49
2 0.54 1.00 0.51 0.50 0.55 0.51 0.47 0.47
3 0.56 0.51 1.00 0.55 0.60 0.51 0.49 0.51
4 0.50 0.50 0.55 1.00 0.59 0.55 0.64 0.50
5 0.50 0.55 0.60 0.59 1.00 0.56 0.56 0.53
6 0.51 0.51 0.51 0.55 0.56 1.00 0.63 0.50
7 0.49 0.47 0.49 0.64 0.56 0.63 1.00 0.51
8 0.49 0.47 0.51 0.50 0.53 0.50 0.51 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