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Status: Done started: 2019-Dec-11 14:11:49 UTC
Project Name1f4i
SequenceQEKEAIERLKALGFEESLVIQAYFACEKNENLAANFLLSQNFDDE
Secondary structure

CCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2019-Dec-11 20:59 UTC

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

Cluster #123456789
Cluster density18.817.38.78.54.83.42.32.11.7
Cluster size1205853542217141210
Average cluster RMSD6.43.46.16.44.65.16.05.95.9

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.

#123456789
1 0.00 9.18 9.27 8.77 9.24 12.90 10.10 9.46 9.01
2 9.18 0.00 4.46 9.47 2.50 11.00 9.51 9.23 8.47
3 9.27 4.46 0.00 8.49 5.09 10.80 9.96 7.70 8.13
4 8.77 9.47 8.49 0.00 9.68 10.10 9.49 7.04 10.10
5 9.24 2.50 5.09 9.68 0.00 9.86 8.37 9.26 9.43
6 12.90 11.00 10.80 10.10 9.86 0.00 5.70 9.69 12.70
7 10.10 9.51 9.96 9.49 8.37 5.70 0.00 10.40 12.20
8 9.46 9.23 7.70 7.04 9.26 9.69 10.40 0.00 7.88
9 9.01 8.47 8.13 10.10 9.43 12.70 12.20 7.88 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 0.53 0.47 0.44 0.48 0.43 0.46 0.41 0.37
2 0.53 1.00 0.52 0.43 0.73 0.45 0.46 0.35 0.35
3 0.47 0.52 1.00 0.43 0.50 0.42 0.41 0.39 0.39
4 0.44 0.43 0.43 1.00 0.39 0.37 0.44 0.39 0.37
5 0.48 0.73 0.50 0.39 1.00 0.44 0.47 0.35 0.34
6 0.43 0.45 0.42 0.37 0.44 1.00 0.48 0.40 0.36
7 0.46 0.46 0.41 0.44 0.47 0.48 1.00 0.37 0.35
8 0.41 0.35 0.39 0.39 0.35 0.40 0.37 1.00 0.37
9 0.37 0.35 0.39 0.37 0.34 0.36 0.35 0.37 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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