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Status: Done started: 2016-Mar-29 16:40:42 UTC
Project Nameseq20
SequenceIPPPLPPKPRISSYPEDNFPDEEKASTIKHCPDSESRAPQILR
Secondary structure

CCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Mar-30 00:30 UTC

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

Cluster #123456789
Cluster density9.88.68.36.36.25.85.03.53.4
Cluster size446241464144352324
Average cluster RMSD4.57.25.07.36.67.67.06.67.1

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 14.80 6.10 13.50 10.10 10.50 13.20 13.00 10.10
2 14.80 0.00 12.40 8.41 8.79 7.97 7.95 9.09 10.40
3 6.10 12.40 0.00 10.80 6.15 9.56 12.90 10.00 9.98
4 13.50 8.41 10.80 0.00 8.53 9.03 8.80 9.87 10.10
5 10.10 8.79 6.15 8.53 0.00 9.03 11.30 6.84 10.20
6 10.50 7.97 9.56 9.03 9.03 0.00 7.10 10.20 10.10
7 13.20 7.95 12.90 8.80 11.30 7.10 0.00 12.20 8.66
8 13.00 9.09 10.00 9.87 6.84 10.20 12.20 0.00 12.10
9 10.10 10.40 9.98 10.10 10.20 10.10 8.66 12.10 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 0.48 0.73 0.26 0.63 0.43 0.30 0.28 0.49
2 0.48 1.00 0.50 0.27 0.52 0.48 0.35 0.28 0.31
3 0.73 0.50 1.00 0.28 0.69 0.44 0.28 0.29 0.50
4 0.26 0.27 0.28 1.00 0.32 0.32 0.28 0.33 0.34
5 0.63 0.52 0.69 0.32 1.00 0.44 0.29 0.31 0.44
6 0.43 0.48 0.44 0.32 0.44 1.00 0.34 0.32 0.35
7 0.30 0.35 0.28 0.28 0.29 0.34 1.00 0.28 0.35
8 0.28 0.28 0.29 0.33 0.31 0.32 0.28 1.00 0.32
9 0.49 0.31 0.50 0.34 0.44 0.35 0.35 0.32 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