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Status: Done started: 2015-Dec-21 08:51:05 UTC
Project Namelin03
SequenceMAAAAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGLESEELEPEELLLEPEPEPEPEEEPPRP RAPPGAPGPGPGSGAPGSQEEEEEPGLVEGDPGDGAIEDP
Secondary structure

CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2015-Dec-21 21:36 UTC

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

Cluster #12345678910
Cluster density11.26.73.12.92.32.21.71.71.20.9
Cluster size78674630292924251913
Average cluster RMSD7.010.014.810.512.512.914.214.515.214.4

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.

#12345678910
1 0.00 15.20 19.60 13.60 13.60 12.10 21.50 21.30 19.50 19.10
2 15.20 0.00 16.90 14.10 11.60 15.80 16.50 16.70 18.60 19.10
3 19.60 16.90 0.00 16.80 17.80 22.00 22.20 14.30 21.30 19.90
4 13.60 14.10 16.80 0.00 15.10 17.30 19.50 20.10 19.40 22.70
5 13.60 11.60 17.80 15.10 0.00 16.10 20.10 21.20 14.90 18.20
6 12.10 15.80 22.00 17.30 16.10 0.00 22.20 23.80 21.30 18.80
7 21.50 16.50 22.20 19.50 20.10 22.20 0.00 20.10 19.10 22.40
8 21.30 16.70 14.30 20.10 21.20 23.80 20.10 0.00 22.00 21.40
9 19.50 18.60 21.30 19.40 14.90 21.30 19.10 22.00 0.00 18.10
10 19.10 19.10 19.90 22.70 18.20 18.80 22.40 21.40 18.10 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.

#12345678910
1 1.00 0.31 0.21 0.32 0.26 0.30 0.19 0.17 0.16 0.17
2 0.31 1.00 0.23 0.33 0.32 0.26 0.18 0.20 0.17 0.19
3 0.21 0.23 1.00 0.23 0.20 0.20 0.17 0.18 0.16 0.22
4 0.32 0.33 0.23 1.00 0.23 0.27 0.18 0.17 0.16 0.17
5 0.26 0.32 0.20 0.23 1.00 0.26 0.17 0.21 0.18 0.20
6 0.30 0.26 0.20 0.27 0.26 1.00 0.17 0.17 0.16 0.17
7 0.19 0.18 0.17 0.18 0.17 0.17 1.00 0.20 0.16 0.18
8 0.17 0.20 0.18 0.17 0.21 0.17 0.20 1.00 0.17 0.21
9 0.16 0.17 0.16 0.16 0.18 0.16 0.16 0.17 1.00 0.17
10 0.17 0.19 0.22 0.17 0.20 0.17 0.18 0.21 0.17 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