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Status: Done started: 2019-Dec-11 20:28:23 UTC
Project Name1bhi
SequenceMSDDKPFLCTAPGCGQRFTNEDHLAVHKHKHEMTLKFG
Secondary structure

CCCCCCEECCCCCCCCEECCHHHHHHHHHHHHCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2019-Dec-12 02:12 UTC

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

Cluster #123456789
Cluster density19.115.610.810.05.53.22.92.72.5
Cluster size966659532816161313
Average cluster RMSD5.04.25.55.35.15.15.54.95.1

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 6.85 4.99 4.93 4.86 9.64 7.70 8.67 14.00
2 6.85 0.00 8.82 8.68 6.45 7.83 9.99 8.47 13.10
3 4.99 8.82 0.00 4.63 7.01 11.00 8.01 11.00 15.80
4 4.93 8.68 4.63 0.00 6.35 10.80 7.55 10.80 14.70
5 4.86 6.45 7.01 6.35 0.00 6.66 6.23 6.93 10.60
6 9.64 7.83 11.00 10.80 6.66 0.00 8.10 7.26 7.93
7 7.70 9.99 8.01 7.55 6.23 8.10 0.00 9.99 10.70
8 8.67 8.47 11.00 10.80 6.93 7.26 9.99 0.00 9.58
9 14.00 13.10 15.80 14.70 10.60 7.93 10.70 9.58 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 0.60 0.63 0.68 0.46 0.51 0.53 0.49
2 0.53 1.00 0.56 0.53 0.55 0.48 0.44 0.55 0.49
3 0.60 0.56 1.00 0.65 0.59 0.45 0.49 0.49 0.43
4 0.63 0.53 0.65 1.00 0.60 0.45 0.47 0.50 0.45
5 0.68 0.55 0.59 0.60 1.00 0.50 0.49 0.54 0.51
6 0.46 0.48 0.45 0.45 0.50 1.00 0.42 0.49 0.49
7 0.51 0.44 0.49 0.47 0.49 0.42 1.00 0.41 0.41
8 0.53 0.55 0.49 0.50 0.54 0.49 0.41 1.00 0.53
9 0.49 0.49 0.43 0.45 0.51 0.49 0.41 0.53 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