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Status: Done started: 2016-Aug-16 11:02:10 UTC
Project NameL268-P349_consensus
SequenceLEEKKGNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHI LP
Secondary structure

CCCCCCCEEECCCCCEEEECCCCCEEECCCCEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCEEEECCEEE CC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2016-Aug-16 21:09 UTC

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

Cluster #123456789
Cluster density18.312.011.010.410.46.15.54.63.2
Cluster size635675494919181813
Average cluster RMSD3.44.76.84.74.73.13.33.94.1

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 7.77 9.17 13.00 16.20 12.10 11.30 17.40 14.50
2 7.77 0.00 9.56 12.00 15.90 12.70 12.20 16.60 13.80
3 9.17 9.56 0.00 9.96 15.40 15.30 12.20 14.80 15.10
4 13.00 12.00 9.96 0.00 16.10 16.30 13.20 14.50 16.60
5 16.20 15.90 15.40 16.10 0.00 12.30 17.50 17.60 8.77
6 12.10 12.70 15.30 16.30 12.30 0.00 12.20 18.20 8.85
7 11.30 12.20 12.20 13.20 17.50 12.20 0.00 15.80 16.70
8 17.40 16.60 14.80 14.50 17.60 18.20 15.80 0.00 19.10
9 14.50 13.80 15.10 16.60 8.77 8.85 16.70 19.10 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 0.36 0.36 0.27 0.21 0.34 0.23 0.23 0.25
2 0.36 1.00 0.27 0.23 0.21 0.27 0.20 0.22 0.23
3 0.36 0.27 1.00 0.28 0.20 0.25 0.22 0.22 0.25
4 0.27 0.23 0.28 1.00 0.22 0.21 0.18 0.18 0.22
5 0.21 0.21 0.20 0.22 1.00 0.30 0.25 0.23 0.30
6 0.34 0.27 0.25 0.21 0.30 1.00 0.26 0.23 0.44
7 0.23 0.20 0.22 0.18 0.25 0.26 1.00 0.36 0.20
8 0.23 0.22 0.22 0.18 0.23 0.23 0.36 1.00 0.27
9 0.25 0.23 0.25 0.22 0.30 0.44 0.20 0.27 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