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Status: Done started: 2015-Sep-09 12:06:34 UTC
Project Nametest-cf-5
SequenceAREVILAVHGMTCSACTNTINTQLRALKGVTKCDISLVTNECQVTYDNEVTADSIKEIIEDCGFDCEILRDS
Secondary structure

CEEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Sep-09 22:16 UTC

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

Cluster #123456789
Cluster density25.918.94.52.82.11.71.70.90.5
Cluster size116104453121141784
Average cluster RMSD4.55.510.111.110.08.410.28.97.5

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 5.93 14.90 12.50 18.60 14.90 17.20 18.30 21.40
2 5.93 0.00 15.00 13.30 18.80 16.60 16.90 17.40 18.70
3 14.90 15.00 0.00 15.40 16.90 16.40 17.70 17.30 17.80
4 12.50 13.30 15.40 0.00 14.40 14.90 15.50 13.10 15.30
5 18.60 18.80 16.90 14.40 0.00 12.70 16.00 11.40 11.90
6 14.90 16.60 16.40 14.90 12.70 0.00 15.40 13.30 15.40
7 17.20 16.90 17.70 15.50 16.00 15.40 0.00 15.30 18.40
8 18.30 17.40 17.30 13.10 11.40 13.30 15.30 0.00 17.00
9 21.40 18.70 17.80 15.30 11.90 15.40 18.40 17.00 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 0.46 0.24 0.33 0.24 0.43 0.27 0.24 0.25
2 0.46 1.00 0.27 0.28 0.25 0.39 0.23 0.24 0.25
3 0.24 0.27 1.00 0.24 0.21 0.23 0.25 0.23 0.23
4 0.33 0.28 0.24 1.00 0.26 0.27 0.21 0.24 0.30
5 0.24 0.25 0.21 0.26 1.00 0.29 0.23 0.27 0.27
6 0.43 0.39 0.23 0.27 0.29 1.00 0.26 0.24 0.29
7 0.27 0.23 0.25 0.21 0.23 0.26 1.00 0.26 0.25
8 0.24 0.24 0.23 0.24 0.27 0.24 0.26 1.00 0.23
9 0.25 0.25 0.23 0.30 0.27 0.29 0.25 0.23 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