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Status: Done started: 2019-Dec-19 05:01:38 UTC
Project Name1bhi_r2
SequenceMSDDKPFLCTAPGCGQRFTNEDHLAVHKHKHEMTLKFG
Secondary structure

CCCCCCEECCCCCCCCEECCHHHHHHHHHHHHCCCCCC

Simulation (CABS) temperature2.5 - 1.0
Estimated finish time2019-Dec-19 11:22 UTC

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

Cluster #123456789
Cluster density14.012.811.511.39.99.38.81.81.7
Cluster size6645534347424798
Average cluster RMSD4.73.54.63.84.74.55.45.04.7

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 5.65 5.60 7.42 4.58 6.89 6.70 8.14 8.43
2 5.65 0.00 8.67 4.48 7.17 10.60 8.85 10.40 8.29
3 5.60 8.67 0.00 10.40 4.37 4.03 5.83 7.92 9.90
4 7.42 4.48 10.40 0.00 8.14 11.80 8.77 10.20 7.81
5 4.58 7.17 4.37 8.14 0.00 5.37 5.54 6.87 8.78
6 6.89 10.60 4.03 11.80 5.37 0.00 6.58 7.76 11.20
7 6.70 8.85 5.83 8.77 5.54 6.58 0.00 8.64 9.80
8 8.14 10.40 7.92 10.20 6.87 7.76 8.64 0.00 8.67
9 8.43 8.29 9.90 7.81 8.78 11.20 9.80 8.67 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 0.55 0.59 0.55 0.62 0.49 0.51 0.55 0.49
2 0.55 1.00 0.53 0.68 0.58 0.49 0.51 0.54 0.51
3 0.59 0.53 1.00 0.56 0.66 0.66 0.62 0.56 0.52
4 0.55 0.68 0.56 1.00 0.58 0.50 0.53 0.54 0.53
5 0.62 0.58 0.66 0.58 1.00 0.57 0.64 0.57 0.51
6 0.49 0.49 0.66 0.50 0.57 1.00 0.60 0.53 0.47
7 0.51 0.51 0.62 0.53 0.64 0.60 1.00 0.55 0.48
8 0.55 0.54 0.56 0.54 0.57 0.53 0.55 1.00 0.47
9 0.49 0.51 0.52 0.53 0.51 0.47 0.48 0.47 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