Download models Download trajectory View trajectory
Status: Done started: 2013-Dec-02 12:15:35 UTC
Project Namemt-loop-w
SequenceFTGEEDIEDGWKPEG
Secondary structure

CCCHHHCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2013-Dec-02 15:46 UTC

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

Cluster #123456789
Cluster density52.518.112.512.211.19.28.77.34.0
Cluster size1245134383126262010
Average cluster RMSD2.42.82.73.12.82.83.02.72.5

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 3.45 3.68 4.00 5.35 4.68 3.56 4.93 5.72
2 3.45 0.00 2.32 2.78 4.24 3.99 4.31 3.18 5.40
3 3.68 2.32 0.00 3.71 4.95 3.73 4.03 3.29 4.51
4 4.00 2.78 3.71 0.00 3.73 4.37 4.95 4.62 6.74
5 5.35 4.24 4.95 3.73 0.00 3.66 5.77 4.41 7.01
6 4.68 3.99 3.73 4.37 3.66 0.00 4.21 3.87 5.41
7 3.56 4.31 4.03 4.95 5.77 4.21 0.00 4.55 4.78
8 4.93 3.18 3.29 4.62 4.41 3.87 4.55 0.00 4.27
9 5.72 5.40 4.51 6.74 7.01 5.41 4.78 4.27 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 0.73 0.68 0.63 0.45 0.52 0.68 0.65 0.42
2 0.73 1.00 0.75 0.75 0.50 0.48 0.60 0.65 0.47
3 0.68 0.75 1.00 0.68 0.52 0.53 0.63 0.62 0.57
4 0.63 0.75 0.68 1.00 0.55 0.53 0.55 0.58 0.47
5 0.45 0.50 0.52 0.55 1.00 0.55 0.45 0.57 0.48
6 0.52 0.48 0.53 0.53 0.55 1.00 0.52 0.55 0.65
7 0.68 0.60 0.63 0.55 0.45 0.52 1.00 0.48 0.47
8 0.65 0.65 0.62 0.58 0.57 0.55 0.48 1.00 0.55
9 0.42 0.47 0.57 0.47 0.48 0.65 0.47 0.55 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