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Status: Done started: 2016-Mar-30 10:16:31 UTC
Project Nameseq48
SequenceNQVVQFETINLNSASSWFTEIGAGSQQLDSIHVTQLERDTVLVCL
Secondary structure

CCEEEEEEECCCCCCCCEEECCCCCCEECEEEEEECCCCEEEEEC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Mar-30 18:47 UTC

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

Cluster #12345678910
Cluster density30.326.615.63.32.92.82.61.21.00.7
Cluster size767097272421231084
Average cluster RMSD2.52.66.28.28.27.58.98.27.85.6

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.

#12345678910
1 0.00 4.67 3.66 11.40 14.30 14.30 12.30 14.50 17.90 16.10
2 4.67 0.00 5.46 12.00 13.70 13.20 12.70 13.60 18.60 15.50
3 3.66 5.46 0.00 11.80 14.10 13.10 11.30 13.70 18.80 16.80
4 11.40 12.00 11.80 0.00 12.10 14.40 10.40 13.30 15.50 11.70
5 14.30 13.70 14.10 12.10 0.00 10.50 10.20 13.10 13.70 13.00
6 14.30 13.20 13.10 14.40 10.50 0.00 13.00 11.60 15.10 11.30
7 12.30 12.70 11.30 10.40 10.20 13.00 0.00 12.20 14.20 14.90
8 14.50 13.60 13.70 13.30 13.10 11.60 12.20 0.00 17.80 12.20
9 17.90 18.60 18.80 15.50 13.70 15.10 14.20 17.80 0.00 16.70
10 16.10 15.50 16.80 11.70 13.00 11.30 14.90 12.20 16.70 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.

#12345678910
1 1.00 0.55 0.59 0.28 0.23 0.35 0.29 0.24 0.30 0.28
2 0.55 1.00 0.48 0.23 0.25 0.28 0.24 0.27 0.29 0.29
3 0.59 0.48 1.00 0.28 0.26 0.37 0.30 0.26 0.34 0.27
4 0.28 0.23 0.28 1.00 0.27 0.28 0.25 0.29 0.30 0.28
5 0.23 0.25 0.26 0.27 1.00 0.28 0.28 0.25 0.29 0.25
6 0.35 0.28 0.37 0.28 0.28 1.00 0.25 0.30 0.27 0.26
7 0.29 0.24 0.30 0.25 0.28 0.25 1.00 0.27 0.29 0.27
8 0.24 0.27 0.26 0.29 0.25 0.30 0.27 1.00 0.28 0.26
9 0.30 0.29 0.34 0.30 0.29 0.27 0.29 0.28 1.00 0.28
10 0.28 0.29 0.27 0.28 0.25 0.26 0.27 0.26 0.28 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