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Status: Done started: 2016-Mar-29 04:31:03 UTC
Project Nameseq7
SequenceKRKSFIGTPYWMAPEVAAVEKNGGYNQLCDIWAVGITAIELGELQPPMFDLH
Secondary structure

CCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHEHHHCCEEEECCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Mar-29 13:55 UTC

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

Cluster #123456789
Cluster density18.214.46.44.62.92.11.71.51.0
Cluster size1041054734241712116
Average cluster RMSD5.77.37.37.48.38.17.27.46.1

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 5.68 5.53 10.70 8.47 12.30 13.70 15.40 16.50
2 5.68 0.00 7.24 9.84 10.30 10.80 13.20 17.00 16.50
3 5.53 7.24 0.00 9.22 7.57 13.40 12.90 15.20 16.40
4 10.70 9.84 9.22 0.00 11.60 11.90 12.10 14.40 16.50
5 8.47 10.30 7.57 11.60 0.00 12.10 12.90 15.10 16.40
6 12.30 10.80 13.40 11.90 12.10 0.00 12.50 14.80 14.60
7 13.70 13.20 12.90 12.10 12.90 12.50 0.00 11.10 13.50
8 15.40 17.00 15.20 14.40 15.10 14.80 11.10 0.00 9.14
9 16.50 16.50 16.40 16.50 16.40 14.60 13.50 9.14 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 0.48 0.46 0.35 0.46 0.38 0.25 0.25 0.29
2 0.48 1.00 0.45 0.37 0.36 0.35 0.26 0.26 0.24
3 0.46 0.45 1.00 0.39 0.39 0.30 0.29 0.27 0.29
4 0.35 0.37 0.39 1.00 0.31 0.30 0.27 0.26 0.26
5 0.46 0.36 0.39 0.31 1.00 0.33 0.27 0.26 0.24
6 0.38 0.35 0.30 0.30 0.33 1.00 0.28 0.28 0.30
7 0.25 0.26 0.29 0.27 0.27 0.28 1.00 0.23 0.25
8 0.25 0.26 0.27 0.26 0.26 0.28 0.23 1.00 0.35
9 0.29 0.24 0.29 0.26 0.24 0.30 0.25 0.35 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