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Status: Done started: 2017-Aug-28 11:04:05 UTC
Project Namegymnema_ILP_1
SequenceYISPHCLWYLVEHFLILVCHSRGFFFTTKYTFVEWLMHLQSDTYPNAATLV
Secondary structure

CCCCHHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Aug-28 18:14 UTC

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

Cluster #123456789
Cluster density21.815.87.16.25.04.23.93.11.7
Cluster size789545382627251610
Average cluster RMSD3.66.06.36.25.26.46.55.26.0

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 10.50 10.30 4.38 11.30 13.00 10.10 13.30 11.80
2 10.50 0.00 4.02 10.10 6.57 8.16 5.55 8.96 7.45
3 10.30 4.02 0.00 9.60 6.27 8.55 5.03 9.28 7.60
4 4.38 10.10 9.60 0.00 10.80 11.30 10.40 12.40 11.20
5 11.30 6.57 6.27 10.80 0.00 7.26 8.63 8.28 9.31
6 13.00 8.16 8.55 11.30 7.26 0.00 9.14 5.62 9.27
7 10.10 5.55 5.03 10.40 8.63 9.14 0.00 9.20 5.03
8 13.30 8.96 9.28 12.40 8.28 5.62 9.20 0.00 8.53
9 11.80 7.45 7.60 11.20 9.31 9.27 5.03 8.53 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 0.44 0.47 0.68 0.41 0.41 0.44 0.44 0.46
2 0.44 1.00 0.58 0.39 0.46 0.48 0.55 0.54 0.51
3 0.47 0.58 1.00 0.46 0.47 0.50 0.59 0.52 0.53
4 0.68 0.39 0.46 1.00 0.40 0.41 0.44 0.41 0.42
5 0.41 0.46 0.47 0.40 1.00 0.47 0.43 0.49 0.44
6 0.41 0.48 0.50 0.41 0.47 1.00 0.50 0.54 0.50
7 0.44 0.55 0.59 0.44 0.43 0.50 1.00 0.54 0.66
8 0.44 0.54 0.52 0.41 0.49 0.54 0.54 1.00 0.57
9 0.46 0.51 0.53 0.42 0.44 0.50 0.66 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