Download models Download trajectory View trajectory
Status: Done started: 2017-Aug-28 10:12:21 UTC
Project Namegymnema_ILP
SequenceYISPHCLWYLVEHFLILVCHSRGFFFTTKYTFVEWLMHLQSDTYPNAATLV
Secondary structure

CCCCHHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Aug-28 17:29 UTC

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

Cluster #123456789
Cluster density21.017.47.44.13.93.62.72.40.5
Cluster size961064727252418152
Average cluster RMSD4.66.16.46.76.56.76.66.33.9

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 4.25 6.39 6.60 8.27 10.70 7.61 12.50 14.40
2 4.25 0.00 5.55 5.70 6.81 9.67 6.57 11.70 12.80
3 6.39 5.55 0.00 5.16 5.95 10.40 6.30 10.10 11.40
4 6.60 5.70 5.16 0.00 5.85 10.60 7.83 11.80 13.20
5 8.27 6.81 5.95 5.85 0.00 9.92 4.84 11.60 10.80
6 10.70 9.67 10.40 10.60 9.92 0.00 10.90 8.26 14.10
7 7.61 6.57 6.30 7.83 4.84 10.90 0.00 11.40 8.94
8 12.50 11.70 10.10 11.80 11.60 8.26 11.40 0.00 10.70
9 14.40 12.80 11.40 13.20 10.80 14.10 8.94 10.70 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 0.55 0.51 0.52 0.43 0.38 0.54 0.39 0.43
2 0.55 1.00 0.57 0.56 0.50 0.42 0.54 0.41 0.47
3 0.51 0.57 1.00 0.55 0.50 0.39 0.55 0.46 0.53
4 0.52 0.56 0.55 1.00 0.53 0.44 0.55 0.46 0.48
5 0.43 0.50 0.50 0.53 1.00 0.38 0.53 0.39 0.43
6 0.38 0.42 0.39 0.44 0.38 1.00 0.38 0.51 0.40
7 0.54 0.54 0.55 0.55 0.53 0.38 1.00 0.39 0.47
8 0.39 0.41 0.46 0.46 0.39 0.51 0.39 1.00 0.45
9 0.43 0.47 0.53 0.48 0.43 0.40 0.47 0.45 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