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Status: Done started: 2019-Dec-18 23:23:07 UTC
Project Name2k9d_r2
SequenceSVIRSIIKSSRLEEDRKRYLMTLLDDIKGANDLAKFHQMLVKII
Secondary structure

CHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC

Simulation (CABS) temperature2.5 - 1.0
Estimated finish time2019-Dec-19 06:17 UTC

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

Cluster #123456789
Cluster density39.921.213.87.26.54.93.72.70.6
Cluster size1447662261616992
Average cluster RMSD3.63.64.53.62.53.32.43.33.2

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 7.39 7.32 7.83 8.02 7.30 7.14 7.58 8.51
2 7.39 0.00 1.88 3.06 2.83 2.95 8.01 4.53 10.30
3 7.32 1.88 0.00 2.33 2.95 3.55 7.74 3.93 9.94
4 7.83 3.06 2.33 0.00 3.44 4.34 7.84 3.45 9.92
5 8.02 2.83 2.95 3.44 0.00 3.20 7.12 3.68 9.46
6 7.30 2.95 3.55 4.34 3.20 0.00 7.68 5.08 9.80
7 7.14 8.01 7.74 7.84 7.12 7.68 0.00 5.56 5.25
8 7.58 4.53 3.93 3.45 3.68 5.08 5.56 0.00 8.07
9 8.51 10.30 9.94 9.92 9.46 9.80 5.25 8.07 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 0.60 0.58 0.50 0.55 0.58 0.48 0.49 0.52
2 0.60 1.00 0.75 0.69 0.70 0.68 0.47 0.53 0.48
3 0.58 0.75 1.00 0.73 0.69 0.61 0.52 0.57 0.50
4 0.50 0.69 0.73 1.00 0.64 0.57 0.52 0.66 0.50
5 0.55 0.70 0.69 0.64 1.00 0.61 0.54 0.61 0.53
6 0.58 0.68 0.61 0.57 0.61 1.00 0.45 0.53 0.47
7 0.48 0.47 0.52 0.52 0.54 0.45 1.00 0.58 0.56
8 0.49 0.53 0.57 0.66 0.61 0.53 0.58 1.00 0.51
9 0.52 0.48 0.50 0.50 0.53 0.47 0.56 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.


 

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