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Status: Done started: 2016-May-18 21:49:35 UTC
Project Namerial2
SequenceIVHNSIEFWTTAGLFKLTYYSHWILDDSLLHAAGFGPELGQSPGEEGYVPDADIWTLERTHRISVFSRKWNQSTARWLRR LVFQHHHHHHHTRESGCIS
Secondary structure

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHH HHHHCCCCCCCCEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-May-19 08:41 UTC

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

Cluster #12345678910
Cluster density13.99.07.05.95.64.13.31.41.30.6
Cluster size3581624755371311136
Average cluster RMSD2.59.08.98.09.89.03.98.19.99.6

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 18.40 17.20 21.00 19.30 19.30 15.80 14.70 18.80 15.60
2 18.40 0.00 7.63 10.00 9.91 11.60 19.30 15.90 14.70 20.30
3 17.20 7.63 0.00 10.70 9.83 10.00 18.90 14.20 11.90 18.80
4 21.00 10.00 10.70 0.00 12.10 8.00 20.90 18.00 12.80 21.90
5 19.30 9.91 9.83 12.10 0.00 12.00 19.10 14.30 15.70 21.30
6 19.30 11.60 10.00 8.00 12.00 0.00 21.40 17.40 11.80 21.30
7 15.80 19.30 18.90 20.90 19.10 21.40 0.00 12.80 19.90 10.90
8 14.70 15.90 14.20 18.00 14.30 17.40 12.80 0.00 13.10 13.80
9 18.80 14.70 11.90 12.80 15.70 11.80 19.90 13.10 0.00 17.70
10 15.60 20.30 18.80 21.90 21.30 21.30 10.90 13.80 17.70 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 0.34 0.32 0.38 0.33 0.34 0.41 0.29 0.33 0.39
2 0.34 1.00 0.52 0.34 0.35 0.38 0.33 0.35 0.30 0.31
3 0.32 0.52 1.00 0.33 0.38 0.32 0.32 0.28 0.36 0.31
4 0.38 0.34 0.33 1.00 0.36 0.46 0.35 0.26 0.34 0.28
5 0.33 0.35 0.38 0.36 1.00 0.45 0.34 0.32 0.31 0.33
6 0.34 0.38 0.32 0.46 0.45 1.00 0.31 0.33 0.34 0.33
7 0.41 0.33 0.32 0.35 0.34 0.31 1.00 0.36 0.32 0.45
8 0.29 0.35 0.28 0.26 0.32 0.33 0.36 1.00 0.29 0.33
9 0.33 0.30 0.36 0.34 0.31 0.34 0.32 0.29 1.00 0.30
10 0.39 0.31 0.31 0.28 0.33 0.33 0.45 0.33 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