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Status: Done started: 2014-Aug-14 16:41:10 UTC
Project Name272-253_test
SequenceFMGNLRHKCVRNFTALNGTNGSVEADGLVWESLDLYLSDPENYLLKNGTSDVLLCGNSSDAGTCPEGYRCLKAGENPDHG YTSFDSF
Secondary structure

CCCCCCCCEECCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEECCCCCEECCCCCCCCCCCCCCCEEEEECCCCCCC CCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2014-Aug-15 04:39 UTC

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

Cluster #123456789
Cluster density19.75.12.82.01.71.31.01.00.9
Cluster size1686134242215121212
Average cluster RMSD8.512.012.212.213.311.712.312.413.6

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 14.50 12.50 19.30 16.40 19.80 20.80 18.60 19.40
2 14.50 0.00 15.10 17.70 17.90 19.30 20.70 20.50 18.30
3 12.50 15.10 0.00 17.00 16.70 20.00 13.60 12.70 19.70
4 19.30 17.70 17.00 0.00 16.20 14.10 19.80 18.10 18.60
5 16.40 17.90 16.70 16.20 0.00 20.00 18.50 18.00 19.60
6 19.80 19.30 20.00 14.10 20.00 0.00 20.30 21.30 20.20
7 20.80 20.70 13.60 19.80 18.50 20.30 0.00 12.70 18.20
8 18.60 20.50 12.70 18.10 18.00 21.30 12.70 0.00 18.30
9 19.40 18.30 19.70 18.60 19.60 20.20 18.20 18.30 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 0.16 0.31 0.15 0.16 0.16 0.18 0.17 0.15
2 0.16 1.00 0.22 0.15 0.15 0.16 0.17 0.20 0.17
3 0.31 0.22 1.00 0.16 0.16 0.16 0.17 0.19 0.15
4 0.15 0.15 0.16 1.00 0.20 0.17 0.12 0.16 0.14
5 0.16 0.15 0.16 0.20 1.00 0.19 0.14 0.15 0.14
6 0.16 0.16 0.16 0.17 0.19 1.00 0.15 0.15 0.15
7 0.18 0.17 0.17 0.12 0.14 0.15 1.00 0.15 0.16
8 0.17 0.20 0.19 0.16 0.15 0.15 0.15 1.00 0.14
9 0.15 0.17 0.15 0.14 0.14 0.15 0.16 0.14 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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