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Status: Done started: 2015-May-21 02:37:42 UTC
Project NameGA98_ccc_tr1
SequenceTTYKLILNLKQAKEEAIKELVDAGTAEKYFKLIANAKTVEGVWTLKDEIKTFTVTE
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-May-21 10:10 UTC

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

Cluster #123456789
Cluster density21.56.44.03.92.81.81.81.3Inf
Cluster size155604133251716121
Average cluster RMSD7.29.310.28.48.99.39.19.40.0

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 9.76 12.50 10.30 14.20 14.90 15.60 20.30 25.00
2 9.76 0.00 11.50 9.70 11.90 13.70 14.90 17.30 25.20
3 12.50 11.50 0.00 13.10 11.80 12.60 11.20 18.10 22.90
4 10.30 9.70 13.10 0.00 16.20 11.80 17.10 17.00 22.90
5 14.20 11.90 11.80 16.20 0.00 17.70 13.50 19.60 22.80
6 14.90 13.70 12.60 11.80 17.70 0.00 14.50 14.20 21.40
7 15.60 14.90 11.20 17.10 13.50 14.50 0.00 18.80 19.10
8 20.30 17.30 18.10 17.00 19.60 14.20 18.80 0.00 18.50
9 25.00 25.20 22.90 22.90 22.80 21.40 19.10 18.50 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 0.33 0.25 0.45 0.22 0.25 0.22 0.20 0.20
2 0.33 1.00 0.25 0.30 0.25 0.24 0.24 0.20 0.19
3 0.25 0.25 1.00 0.23 0.25 0.23 0.24 0.21 0.19
4 0.45 0.30 0.23 1.00 0.24 0.24 0.20 0.21 0.20
5 0.22 0.25 0.25 0.24 1.00 0.19 0.24 0.20 0.22
6 0.25 0.24 0.23 0.24 0.19 1.00 0.20 0.24 0.21
7 0.22 0.24 0.24 0.20 0.24 0.20 1.00 0.21 0.22
8 0.20 0.20 0.21 0.21 0.20 0.24 0.21 1.00 0.25
9 0.20 0.19 0.19 0.20 0.22 0.21 0.22 0.25 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