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Status: Done started: 2016-Apr-08 08:50:17 UTC
Project Nameseq1
SequenceMTSLFSLQLLSTQDLAMGWSCII
Secondary structure

CCCEEEEECCCCCCHHCEEEEEC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Apr-08 15:02 UTC

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

Cluster #12345678910
Cluster density32.122.415.712.810.610.59.86.23.01.5
Cluster size6453374340473721126
Average cluster RMSD2.02.42.43.43.84.53.83.44.03.9

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.

#12345678910
1 0.00 2.47 2.55 3.36 4.66 6.25 4.18 4.92 7.78 9.83
2 2.47 0.00 2.76 3.05 4.98 5.69 3.62 5.59 6.81 10.20
3 2.55 2.76 0.00 3.23 4.80 5.40 3.41 5.20 7.04 9.55
4 3.36 3.05 3.23 0.00 4.02 4.64 3.29 4.61 6.37 8.86
5 4.66 4.98 4.80 4.02 0.00 4.69 4.20 3.38 6.16 7.35
6 6.25 5.69 5.40 4.64 4.69 0.00 4.21 5.75 4.87 8.42
7 4.18 3.62 3.41 3.29 4.20 4.21 0.00 5.51 4.97 8.84
8 4.92 5.59 5.20 4.61 3.38 5.75 5.51 0.00 7.24 6.33
9 7.78 6.81 7.04 6.37 6.16 4.87 4.97 7.24 0.00 8.45
10 9.83 10.20 9.55 8.86 7.35 8.42 8.84 6.33 8.45 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.

#12345678910
1 1.00 0.69 0.84 0.63 0.45 0.39 0.52 0.51 0.35 0.37
2 0.69 1.00 0.68 0.64 0.46 0.45 0.56 0.43 0.41 0.37
3 0.84 0.68 1.00 0.61 0.50 0.46 0.56 0.50 0.37 0.40
4 0.63 0.64 0.61 1.00 0.55 0.49 0.60 0.51 0.42 0.39
5 0.45 0.46 0.50 0.55 1.00 0.51 0.51 0.65 0.40 0.45
6 0.39 0.45 0.46 0.49 0.51 1.00 0.53 0.42 0.53 0.43
7 0.52 0.56 0.56 0.60 0.51 0.53 1.00 0.48 0.46 0.43
8 0.51 0.43 0.50 0.51 0.65 0.42 0.48 1.00 0.40 0.45
9 0.35 0.41 0.37 0.42 0.40 0.53 0.46 0.40 1.00 0.41
10 0.37 0.37 0.40 0.39 0.45 0.43 0.43 0.45 0.41 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