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Status: Done started: 2014-Dec-04 16:24:09 UTC
Project Nameseq5
SequenceVKDTIKKDMLFLKGGTDDMHNFVHRFNEIAENMKKVS
Secondary structure

CHHHHHHHEEEEECCCCHHHHHHHHHHHHHHHCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2014-Dec-04 22:32 UTC

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

Cluster #123456789
Cluster density38.221.521.37.96.95.93.02.42.2
Cluster size118607427252612108
Average cluster RMSD3.12.83.53.43.64.44.04.23.7

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 2.38 2.11 4.40 4.43 3.95 6.98 12.30 10.40
2 2.38 0.00 2.63 5.40 4.57 3.66 8.11 13.30 11.70
3 2.11 2.63 0.00 3.81 4.19 4.07 6.29 11.60 10.10
4 4.40 5.40 3.81 0.00 4.74 4.82 5.33 10.70 8.61
5 4.43 4.57 4.19 4.74 0.00 3.44 6.96 11.00 9.71
6 3.95 3.66 4.07 4.82 3.44 0.00 8.13 12.90 11.10
7 6.98 8.11 6.29 5.33 6.96 8.13 0.00 6.86 4.92
8 12.30 13.30 11.60 10.70 11.00 12.90 6.86 0.00 5.54
9 10.40 11.70 10.10 8.61 9.71 11.10 4.92 5.54 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 0.76 0.78 0.69 0.74 0.67 0.59 0.52 0.59
2 0.76 1.00 0.72 0.64 0.69 0.72 0.60 0.48 0.55
3 0.78 0.72 1.00 0.69 0.78 0.66 0.64 0.51 0.57
4 0.69 0.64 0.69 1.00 0.69 0.60 0.69 0.52 0.64
5 0.74 0.69 0.78 0.69 1.00 0.72 0.62 0.51 0.58
6 0.67 0.72 0.66 0.60 0.72 1.00 0.54 0.51 0.51
7 0.59 0.60 0.64 0.69 0.62 0.54 1.00 0.53 0.64
8 0.52 0.48 0.51 0.52 0.51 0.51 0.53 1.00 0.53
9 0.59 0.55 0.57 0.64 0.58 0.51 0.64 0.53 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