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Status: Done started: 2020-Jun-03 19:27:29 UTC
Project Name1R1F_KW_sec
SequenceTFCGETCRVIPVCTYSAALGCTCDDRSDGLCKRNGDP
Secondary structure

CCCCCCCCCCCCCCCHHHHCCCECCCCCCCECCCCCC

User provided constraintsYes
Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Jun-04 02:33 UTC

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

Cluster #123456789
Cluster density37.47.67.35.54.14.14.03.72.1
Cluster size1634338272120221610
Average cluster RMSD4.45.75.24.95.14.95.54.44.7

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 6.06 7.42 10.10 11.80 10.50 10.60 10.40 11.00
2 6.06 0.00 6.70 8.62 8.20 9.63 10.10 7.55 9.60
3 7.42 6.70 0.00 7.48 8.27 8.49 8.40 5.86 8.56
4 10.10 8.62 7.48 0.00 8.88 8.82 6.51 8.10 10.30
5 11.80 8.20 8.27 8.88 0.00 9.50 8.49 5.39 7.46
6 10.50 9.63 8.49 8.82 9.50 0.00 6.35 10.00 6.39
7 10.60 10.10 8.40 6.51 8.49 6.35 0.00 9.07 8.78
8 10.40 7.55 5.86 8.10 5.39 10.00 9.07 0.00 8.62
9 11.00 9.60 8.56 10.30 7.46 6.39 8.78 8.62 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 0.42 0.49 0.38 0.33 0.30 0.31 0.29 0.31
2 0.42 1.00 0.37 0.30 0.37 0.36 0.33 0.35 0.32
3 0.49 0.37 1.00 0.37 0.34 0.28 0.28 0.35 0.33
4 0.38 0.30 0.37 1.00 0.25 0.28 0.34 0.30 0.26
5 0.33 0.37 0.34 0.25 1.00 0.26 0.32 0.42 0.32
6 0.30 0.36 0.28 0.28 0.26 1.00 0.42 0.25 0.35
7 0.31 0.33 0.28 0.34 0.32 0.42 1.00 0.30 0.29
8 0.29 0.35 0.35 0.30 0.42 0.25 0.30 1.00 0.30
9 0.31 0.32 0.33 0.26 0.32 0.35 0.29 0.30 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