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Status: Done started: 2014-Aug-07 02:17:18 UTC
Project Nameseg1
SequenceMGFLKIGTPLSWDDVQDVKSLIRLYGILQFVHVYKLNKDRYDENIMFGDEIEYIIIRNDESLKESSALLCASDLIDEMMN LESVIDCQYGSHWTPEYSSFTIEGTPSVPFKLDINSSCFV
Secondary structure

CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCCEEEECCCHHHHHHHHC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2014-Aug-07 16:12 UTC

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

Cluster #123456789
Cluster density18.88.25.93.52.41.91.01.00.9
Cluster size116625142322491311
Average cluster RMSD6.27.68.711.913.312.99.312.512.6

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.

#123456789
1 0.00 12.90 10.80 8.75 20.20 19.20 19.60 21.10 19.90
2 12.90 0.00 13.90 16.10 16.60 17.70 19.70 20.40 18.70
3 10.80 13.90 0.00 11.30 17.30 18.50 21.90 19.20 20.90
4 8.75 16.10 11.30 0.00 18.50 19.80 19.80 20.90 18.00
5 20.20 16.60 17.30 18.50 0.00 15.00 19.50 14.20 19.00
6 19.20 17.70 18.50 19.80 15.00 0.00 14.90 16.00 18.30
7 19.60 19.70 21.90 19.80 19.50 14.90 0.00 18.80 21.40
8 21.10 20.40 19.20 20.90 14.20 16.00 18.80 0.00 17.70
9 19.90 18.70 20.90 18.00 19.00 18.30 21.40 17.70 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.

#123456789
1 1.00 0.34 0.35 0.39 0.25 0.24 0.24 0.27 0.23
2 0.34 1.00 0.30 0.28 0.26 0.25 0.23 0.25 0.19
3 0.35 0.30 1.00 0.37 0.22 0.24 0.24 0.24 0.19
4 0.39 0.28 0.37 1.00 0.25 0.24 0.23 0.27 0.24
5 0.25 0.26 0.22 0.25 1.00 0.25 0.26 0.25 0.23
6 0.24 0.25 0.24 0.24 0.25 1.00 0.29 0.24 0.25
7 0.24 0.23 0.24 0.23 0.26 0.29 1.00 0.21 0.21
8 0.27 0.25 0.24 0.27 0.25 0.24 0.21 1.00 0.24
9 0.23 0.19 0.19 0.24 0.23 0.25 0.21 0.24 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