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Status: Done started: 2015-Nov-30 19:18:49 UTC
Project Nameg6_p8
SequenceSALTIRESNDSTVEVCGLPVAEDLTGTDSAQLAGEGPHAESLEGSLSAVRKSTQAAARIFQAFRVESFHRKKVVEYGDDD CGLSDERTLSLVSLKNVKPGQHDTH
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCC CCCCHHHHHHHHHHCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Dec-01 07:45 UTC

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

Cluster #123456789
Cluster density18.57.63.23.01.71.50.80.60.6
Cluster size13988373321201066
Average cluster RMSD7.511.511.611.112.113.411.810.810.6

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 6.73 10.40 10.80 16.20 15.50 19.30 18.20 22.20
2 6.73 0.00 9.41 13.00 15.20 17.20 19.90 20.90 22.30
3 10.40 9.41 0.00 15.10 13.40 17.60 18.70 20.50 21.40
4 10.80 13.00 15.10 0.00 17.90 14.60 16.80 19.10 19.10
5 16.20 15.20 13.40 17.90 0.00 17.70 16.30 18.90 18.00
6 15.50 17.20 17.60 14.60 17.70 0.00 18.90 13.20 18.70
7 19.30 19.90 18.70 16.80 16.30 18.90 0.00 23.70 15.50
8 18.20 20.90 20.50 19.10 18.90 13.20 23.70 0.00 22.00
9 22.20 22.30 21.40 19.10 18.00 18.70 15.50 22.00 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 0.46 0.33 0.36 0.30 0.33 0.36 0.28 0.22
2 0.46 1.00 0.33 0.34 0.34 0.35 0.35 0.31 0.23
3 0.33 0.33 1.00 0.38 0.33 0.34 0.28 0.32 0.21
4 0.36 0.34 0.38 1.00 0.31 0.34 0.40 0.30 0.24
5 0.30 0.34 0.33 0.31 1.00 0.36 0.29 0.31 0.24
6 0.33 0.35 0.34 0.34 0.36 1.00 0.31 0.33 0.22
7 0.36 0.35 0.28 0.40 0.29 0.31 1.00 0.28 0.27
8 0.28 0.31 0.32 0.30 0.31 0.33 0.28 1.00 0.24
9 0.22 0.23 0.21 0.24 0.24 0.22 0.27 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