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Status: Done started: 2020-Mar-20 09:27:39 UTC
Project NameAVP1696
SequenceCPFVC
Secondary structure

CCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Mar-20 12:34 UTC

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

Cluster #123456789
Cluster density96.666.866.359.658.632.932.113.512.5
Cluster size605251546233231114
Average cluster RMSD0.60.80.80.91.11.00.70.81.1

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 1.79 0.45 1.74 0.91 1.38 1.72 2.90 1.81
2 1.79 0.00 1.68 0.41 1.23 1.55 0.48 2.52 1.53
3 0.45 1.68 0.00 1.63 0.71 1.31 1.61 2.81 1.74
4 1.74 0.41 1.63 0.00 1.17 1.41 0.64 2.45 1.52
5 0.91 1.23 0.71 1.17 0.00 1.44 1.18 2.62 1.75
6 1.38 1.55 1.31 1.41 1.44 0.00 1.60 2.66 0.90
7 1.72 0.48 1.61 0.64 1.18 1.60 0.00 2.94 1.76
8 2.90 2.52 2.81 2.45 2.62 2.66 2.94 0.00 2.02
9 1.81 1.53 1.74 1.52 1.75 0.90 1.76 2.02 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 0.85 1.00 0.85 0.95 0.80 0.85 0.50 0.70
2 0.85 1.00 0.85 1.00 0.85 0.80 1.00 0.50 0.75
3 1.00 0.85 1.00 0.85 0.95 0.80 0.85 0.45 0.65
4 0.85 1.00 0.85 1.00 0.85 0.80 1.00 0.50 0.75
5 0.95 0.85 0.95 0.85 1.00 0.90 0.85 0.55 0.75
6 0.80 0.80 0.80 0.80 0.90 1.00 0.80 0.65 0.95
7 0.85 1.00 0.85 1.00 0.85 0.80 1.00 0.45 0.75
8 0.50 0.50 0.45 0.50 0.55 0.65 0.45 1.00 0.65
9 0.70 0.75 0.65 0.75 0.75 0.95 0.75 0.65 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.


 

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