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Status: Done started: 2018-Apr-17 16:10:21 UTC
Project NameProtein
SequenceMGQSFNAPYEAIGEELLSQLVDTFYERVASHPLLKPIFPSDLTETARKQKQFLTQYLGGPPLYTEEHGHPMLRARHLPFP ITNERADAWLSCMKDAMDHVGLEGEIREFLFGRLELTARHMVNQTEAEDRSS
Secondary structure

CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCCC CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2018-Apr-18 06:05 UTC

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

Cluster #123456789
Cluster density32.725.611.39.27.24.43.82.50.5
Cluster size70606052313622272
Average cluster RMSD2.12.35.35.74.38.25.710.93.8

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 8.35 12.30 16.80 15.70 11.00 8.27 15.80 20.90
2 8.35 0.00 8.15 17.50 16.70 11.20 7.57 14.50 19.20
3 12.30 8.15 0.00 18.30 20.20 12.20 11.70 14.30 17.90
4 16.80 17.50 18.30 0.00 20.10 14.80 16.50 14.70 15.00
5 15.70 16.70 20.20 20.10 0.00 17.30 15.60 15.50 20.10
6 11.00 11.20 12.20 14.80 17.30 0.00 13.50 13.80 20.40
7 8.27 7.57 11.70 16.50 15.60 13.50 0.00 16.40 18.90
8 15.80 14.50 14.30 14.70 15.50 13.80 16.40 0.00 19.60
9 20.90 19.20 17.90 15.00 20.10 20.40 18.90 19.60 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 0.33 0.27 0.34 0.29 0.28 0.38 0.17 0.24
2 0.33 1.00 0.45 0.30 0.29 0.27 0.36 0.20 0.26
3 0.27 0.45 1.00 0.26 0.27 0.27 0.30 0.16 0.26
4 0.34 0.30 0.26 1.00 0.25 0.26 0.31 0.16 0.26
5 0.29 0.29 0.27 0.25 1.00 0.23 0.25 0.15 0.27
6 0.28 0.27 0.27 0.26 0.23 1.00 0.24 0.20 0.20
7 0.38 0.36 0.30 0.31 0.25 0.24 1.00 0.18 0.36
8 0.17 0.20 0.16 0.16 0.15 0.20 0.18 1.00 0.15
9 0.24 0.26 0.26 0.26 0.27 0.20 0.36 0.15 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