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Status: Done started: 2019-Dec-19 00:41:11 UTC
Project Name2ysg_r2
SequenceGSSGSSGLPYGWEEAYTADGIKYFINHVTQTTSWIHPVMS
Secondary structure

CCCCCCCCCCCEEEEECCCCCEEEEECCCCCEECCCCCCC

Simulation (CABS) temperature2.5 - 1.0
Estimated finish time2019-Dec-19 07:10 UTC

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

Cluster #123456789
Cluster density73.913.712.09.65.04.11.81.40.6
Cluster size12367445124271194
Average cluster RMSD1.74.93.75.34.86.66.06.36.3

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 7.61 3.00 6.91 9.12 6.40 10.90 12.10 12.40
2 7.61 0.00 8.01 4.04 3.93 5.91 8.57 11.10 10.00
3 3.00 8.01 0.00 7.28 9.36 6.51 10.90 11.90 12.20
4 6.91 4.04 7.28 0.00 5.66 5.89 7.57 10.90 10.20
5 9.12 3.93 9.36 5.66 0.00 7.46 9.83 11.30 10.00
6 6.40 5.91 6.51 5.89 7.46 0.00 9.78 11.10 9.81
7 10.90 8.57 10.90 7.57 9.83 9.78 0.00 8.11 10.90
8 12.10 11.10 11.90 10.90 11.30 11.10 8.11 0.00 12.80
9 12.40 10.00 12.20 10.20 10.00 9.81 10.90 12.80 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 0.56 0.72 0.51 0.48 0.41 0.37 0.38 0.26
2 0.56 1.00 0.54 0.54 0.50 0.44 0.42 0.39 0.29
3 0.72 0.54 1.00 0.51 0.46 0.41 0.36 0.36 0.28
4 0.51 0.54 0.51 1.00 0.41 0.38 0.39 0.42 0.32
5 0.48 0.50 0.46 0.41 1.00 0.29 0.34 0.41 0.28
6 0.41 0.44 0.41 0.38 0.29 1.00 0.36 0.32 0.31
7 0.37 0.42 0.36 0.39 0.34 0.36 1.00 0.34 0.32
8 0.38 0.39 0.36 0.42 0.41 0.32 0.34 1.00 0.29
9 0.26 0.29 0.28 0.32 0.28 0.31 0.32 0.29 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