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Status: Done started: 2016-Jan-29 02:59:23 UTC
Project NameCASP9_E
SequenceWNRITAVTMPEISVP
Secondary structure

CCEEEEEEECCEECC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Jan-29 06:30 UTC

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

Cluster #12345678
Cluster density54.935.433.211.68.98.57.67.5
Cluster size10679702619212118
Average cluster RMSD1.92.22.12.22.12.52.82.4

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.

#12345678
1 0.00 2.79 3.63 5.29 9.60 7.55 5.73 9.33
2 2.79 0.00 2.68 4.16 8.22 6.21 4.34 7.57
3 3.63 2.68 0.00 3.15 7.34 5.39 4.43 7.16
4 5.29 4.16 3.15 0.00 5.29 3.48 3.49 5.19
5 9.60 8.22 7.34 5.29 0.00 2.58 5.10 2.80
6 7.55 6.21 5.39 3.48 2.58 0.00 3.26 3.25
7 5.73 4.34 4.43 3.49 5.10 3.26 0.00 4.86
8 9.33 7.57 7.16 5.19 2.80 3.25 4.86 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.

#12345678
1 1.00 0.68 0.62 0.58 0.57 0.58 0.57 0.57
2 0.68 1.00 0.78 0.60 0.58 0.62 0.68 0.60
3 0.62 0.78 1.00 0.68 0.62 0.63 0.62 0.60
4 0.58 0.60 0.68 1.00 0.65 0.70 0.57 0.63
5 0.57 0.58 0.62 0.65 1.00 0.75 0.58 0.75
6 0.58 0.62 0.63 0.70 0.75 1.00 0.67 0.68
7 0.57 0.68 0.62 0.57 0.58 0.67 1.00 0.57
8 0.57 0.60 0.60 0.63 0.75 0.68 0.57 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