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Status: Done started: 2013-Nov-11 14:30:17 UTC
Project NameLongela2
SequencePLVPSQPLVPSQPLVPSQPQPPLPP
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2013-Nov-11 18:56 UTC

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

Cluster #123456789
Cluster density15.413.912.912.07.35.95.45.04.8
Cluster size705858513227242218
Average cluster RMSD4.54.24.54.34.44.54.54.43.7

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 7.30 5.77 8.05 9.41 8.36 6.64 10.10 11.60
2 7.30 0.00 7.20 8.41 6.67 6.01 6.12 5.47 7.15
3 5.77 7.20 0.00 5.54 6.86 5.86 7.06 9.41 9.86
4 8.05 8.41 5.54 0.00 6.50 7.37 9.02 10.50 10.90
5 9.41 6.67 6.86 6.50 0.00 5.47 8.59 7.31 6.53
6 8.36 6.01 5.86 7.37 5.47 0.00 7.00 6.47 6.27
7 6.64 6.12 7.06 9.02 8.59 7.00 0.00 6.04 8.42
8 10.10 5.47 9.41 10.50 7.31 6.47 6.04 0.00 5.06
9 11.60 7.15 9.86 10.90 6.53 6.27 8.42 5.06 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 0.63 0.40 0.35 0.45 0.35 0.38 0.33 0.32
2 0.63 1.00 0.39 0.35 0.41 0.38 0.36 0.41 0.34
3 0.40 0.39 1.00 0.44 0.42 0.46 0.46 0.41 0.39
4 0.35 0.35 0.44 1.00 0.49 0.38 0.35 0.39 0.37
5 0.45 0.41 0.42 0.49 1.00 0.47 0.38 0.44 0.43
6 0.35 0.38 0.46 0.38 0.47 1.00 0.40 0.44 0.45
7 0.38 0.36 0.46 0.35 0.38 0.40 1.00 0.46 0.42
8 0.33 0.41 0.41 0.39 0.44 0.44 0.46 1.00 0.50
9 0.32 0.34 0.39 0.37 0.43 0.45 0.42 0.50 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