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Status: Done started: 2018-Apr-22 23:33:41 UTC
Project NameAM6
SequenceMLYENITETIGNTPLVKLHPNGDDMADVYVKLESFNPGGSVKDRIALNMIQQARKIGQLKEGQAIVEPTSGNTGIGLSMV GAALGHPVTIVMPESFSMERRQIIRAYGATLVLTPASEGMKGAIAKAKEIAKDINGFMPMQFENYWNPTAHFDNTAFEII DELTKSGKRPDMFVAGVGTGGTITGAGHSLKEEFPSIKIVGVESAESPVLSGGEPGPHKIQGISAGFIPQILDMDIIDEI KQVSSEQALETARGTALNEGILVGISSGAAISAAFDKAKALGKGKTIVVIAPDTGERYLSTVLFEGYKY
Secondary structure

CCCCCHHHHHCCCCEEECCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHH HHHCCCCEEEECCCCCCHHHHHHHHHHCCCEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHCCCCHHHHH HHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE EEECCHHHHHHHHHHHHHHCCEEECCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Apr-23 13:28 UTC

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

Cluster #12345678910
Cluster density22.06.75.23.11.91.81.11.10.70.4
Cluster size8957512539382314177
Average cluster RMSD4.18.69.88.020.621.321.613.123.518.5

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 25.90 29.20 21.00 26.40 23.80 29.30 27.50 25.60 40.00
2 25.90 0.00 26.50 26.40 28.40 30.40 27.50 32.90 32.60 37.60
3 29.20 26.50 0.00 25.50 27.50 28.60 27.10 31.80 28.70 40.10
4 21.00 26.40 25.50 0.00 23.00 25.20 30.10 25.90 29.10 36.90
5 26.40 28.40 27.50 23.00 0.00 30.00 28.20 20.90 32.00 37.80
6 23.80 30.40 28.60 25.20 30.00 0.00 30.10 31.40 32.80 36.70
7 29.30 27.50 27.10 30.10 28.20 30.10 0.00 33.10 34.20 34.40
8 27.50 32.90 31.80 25.90 20.90 31.40 33.10 0.00 31.10 41.00
9 25.60 32.60 28.70 29.10 32.00 32.80 34.20 31.10 0.00 41.40
10 40.00 37.60 40.10 36.90 37.80 36.70 34.40 41.00 41.40 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 0.10 0.08 0.10 0.09 0.08 0.07 0.07 0.08 0.07
2 0.10 1.00 0.09 0.10 0.08 0.08 0.08 0.08 0.09 0.07
3 0.08 0.09 1.00 0.08 0.07 0.07 0.08 0.07 0.08 0.06
4 0.10 0.10 0.08 1.00 0.08 0.08 0.07 0.07 0.08 0.07
5 0.09 0.08 0.07 0.08 1.00 0.11 0.06 0.10 0.07 0.07
6 0.08 0.08 0.07 0.08 0.11 1.00 0.07 0.07 0.07 0.07
7 0.07 0.08 0.08 0.07 0.06 0.07 1.00 0.06 0.06 0.06
8 0.07 0.08 0.07 0.07 0.10 0.07 0.06 1.00 0.09 0.07
9 0.08 0.09 0.08 0.08 0.07 0.07 0.06 0.09 1.00 0.07
10 0.07 0.07 0.06 0.07 0.07 0.07 0.06 0.07 0.07 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