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Status: Done started: 2018-Mar-29 04:40:24 UTC
Project NamepolyP
SequencePPPPPPPPPPPPPPPPPPPP
Secondary structure

CCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Mar-29 09:52 UTC

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

Cluster #123456789
Cluster density17.714.713.512.211.611.511.411.38.4
Cluster size594747343736383626
Average cluster RMSD3.33.23.52.83.23.13.33.23.1

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 5.09 7.40 11.30 4.77 8.43 6.06 7.13 8.89
2 5.09 0.00 7.45 10.70 5.12 7.94 8.02 6.02 9.41
3 7.40 7.45 0.00 5.66 4.87 4.30 4.20 5.72 4.36
4 11.30 10.70 5.66 0.00 7.68 4.54 7.31 6.66 3.74
5 4.77 5.12 4.87 7.68 0.00 5.16 4.70 4.40 6.00
6 8.43 7.94 4.30 4.54 5.16 0.00 5.63 4.20 3.97
7 6.06 8.02 4.20 7.31 4.70 5.63 0.00 6.64 5.09
8 7.13 6.02 5.72 6.66 4.40 4.20 6.64 0.00 5.89
9 8.89 9.41 4.36 3.74 6.00 3.97 5.09 5.89 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 0.50 0.47 0.40 0.56 0.47 0.55 0.50 0.49
2 0.50 1.00 0.45 0.47 0.53 0.44 0.45 0.46 0.50
3 0.47 0.45 1.00 0.50 0.53 0.54 0.59 0.44 0.53
4 0.40 0.47 0.50 1.00 0.47 0.55 0.53 0.53 0.61
5 0.56 0.53 0.53 0.47 1.00 0.51 0.49 0.54 0.50
6 0.47 0.44 0.54 0.55 0.51 1.00 0.53 0.59 0.47
7 0.55 0.45 0.59 0.53 0.49 0.53 1.00 0.41 0.51
8 0.50 0.46 0.44 0.53 0.54 0.59 0.41 1.00 0.49
9 0.49 0.50 0.53 0.61 0.50 0.47 0.51 0.49 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