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Status: Done started: 2017-May-14 20:03:35 UTC
Project Namesgs
SequenceMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Secondary structure

CEEEEEECCCCEEEEEECCCCHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-May-15 05:33 UTC

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

Cluster #123456789
Cluster density28.35.83.41.91.61.50.90.90.7
Cluster size182573222201811117
Average cluster RMSD6.49.89.311.312.712.012.211.710.6

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.

#123456789
1 0.00 14.60 15.20 13.80 17.60 16.20 19.60 18.80 19.00
2 14.60 0.00 14.10 14.70 19.10 15.30 20.50 18.00 15.90
3 15.20 14.10 0.00 17.60 16.80 15.00 20.80 20.00 15.50
4 13.80 14.70 17.60 0.00 17.80 15.70 17.30 16.10 16.20
5 17.60 19.10 16.80 17.80 0.00 14.20 15.30 20.40 18.10
6 16.20 15.30 15.00 15.70 14.20 0.00 16.20 18.60 15.80
7 19.60 20.50 20.80 17.30 15.30 16.20 0.00 17.60 23.40
8 18.80 18.00 20.00 16.10 20.40 18.60 17.60 0.00 17.10
9 19.00 15.90 15.50 16.20 18.10 15.80 23.40 17.10 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 0.39 0.23 0.20 0.21 0.20 0.19 0.19 0.18
2 0.39 1.00 0.22 0.21 0.23 0.21 0.20 0.20 0.26
3 0.23 0.22 1.00 0.23 0.20 0.25 0.22 0.23 0.21
4 0.20 0.21 0.23 1.00 0.18 0.22 0.24 0.24 0.19
5 0.21 0.23 0.20 0.18 1.00 0.21 0.22 0.16 0.18
6 0.20 0.21 0.25 0.22 0.21 1.00 0.20 0.17 0.20
7 0.19 0.20 0.22 0.24 0.22 0.20 1.00 0.20 0.24
8 0.19 0.20 0.23 0.24 0.16 0.17 0.20 1.00 0.19
9 0.18 0.26 0.21 0.19 0.18 0.20 0.24 0.19 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