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Status: Done started: 2014-Jan-28 13:03:34 UTC
Project Name280114_1B
SequenceGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTT
Secondary structure

CCCCCCCEEECCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCEECC

User provided constraintsYes
Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2014-Jan-28 20:33 UTC

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

Cluster #123456789
Cluster density22.511.88.85.54.73.83.33.02.8
Cluster size835353423727262019
Average cluster RMSD3.74.56.07.67.97.17.86.76.9

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 4.84 8.52 13.80 11.20 16.50 16.00 14.10 18.00
2 4.84 0.00 6.99 14.00 11.70 15.30 14.20 12.70 17.70
3 8.52 6.99 0.00 11.90 10.00 13.20 13.10 10.10 15.30
4 13.80 14.00 11.90 0.00 12.50 12.90 10.30 8.20 13.30
5 11.20 11.70 10.00 12.50 0.00 9.96 10.30 12.20 10.50
6 16.50 15.30 13.20 12.90 9.96 0.00 8.05 12.50 6.80
7 16.00 14.20 13.10 10.30 10.30 8.05 0.00 10.80 9.56
8 14.10 12.70 10.10 8.20 12.20 12.50 10.80 0.00 14.50
9 18.00 17.70 15.30 13.30 10.50 6.80 9.56 14.50 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 0.58 0.42 0.32 0.30 0.27 0.26 0.28 0.30
2 0.58 1.00 0.48 0.29 0.29 0.29 0.28 0.27 0.28
3 0.42 0.48 1.00 0.32 0.36 0.32 0.30 0.28 0.30
4 0.32 0.29 0.32 1.00 0.26 0.25 0.25 0.34 0.23
5 0.30 0.29 0.36 0.26 1.00 0.36 0.31 0.34 0.32
6 0.27 0.29 0.32 0.25 0.36 1.00 0.28 0.27 0.40
7 0.26 0.28 0.30 0.25 0.31 0.28 1.00 0.28 0.28
8 0.28 0.27 0.28 0.34 0.34 0.27 0.28 1.00 0.26
9 0.30 0.28 0.30 0.23 0.32 0.40 0.28 0.26 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.


 

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