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Status: Done started: 2013-Apr-29 20:04:03 UTC
Project Name2WWEA_dn
SequenceMHHHHHHSSGVDLGTENLYFQSMSIERATILGFSKKSSNLYLIQVTHSNNETSLTEKSFEQFSKLHSQLQKQFASLTLPE FPHWWHLPFTNSDHRRFRDLNHYMEQILNVSHEVTNSDCVLSFFLSE
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEECCEEEEEEECHHHHHHHHHHHHHHCCCCCCCC CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2013-Apr-30 09:59 UTC

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

Cluster #123456789
Cluster density12.37.44.83.12.11.41.10.80.7
Cluster size1106651423023161210
Average cluster RMSD9.08.910.713.514.216.214.315.115.1

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 15.50 13.30 12.50 14.40 19.60 25.00 21.60 24.30
2 15.50 0.00 17.20 17.20 18.60 20.30 21.70 20.40 20.60
3 13.30 17.20 0.00 12.90 7.92 18.40 20.20 19.00 22.10
4 12.50 17.20 12.90 0.00 13.30 19.10 21.60 23.40 21.00
5 14.40 18.60 7.92 13.30 0.00 17.20 19.00 19.40 21.50
6 19.60 20.30 18.40 19.10 17.20 0.00 24.50 21.50 26.10
7 25.00 21.70 20.20 21.60 19.00 24.50 0.00 22.50 18.70
8 21.60 20.40 19.00 23.40 19.40 21.50 22.50 0.00 22.00
9 24.30 20.60 22.10 21.00 21.50 26.10 18.70 22.00 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 0.32 0.27 0.28 0.24 0.17 0.20 0.19 0.17
2 0.32 1.00 0.24 0.20 0.27 0.20 0.18 0.18 0.19
3 0.27 0.24 1.00 0.25 0.46 0.17 0.19 0.16 0.16
4 0.28 0.20 0.25 1.00 0.24 0.19 0.17 0.18 0.18
5 0.24 0.27 0.46 0.24 1.00 0.17 0.19 0.17 0.17
6 0.17 0.20 0.17 0.19 0.17 1.00 0.15 0.16 0.17
7 0.20 0.18 0.19 0.17 0.19 0.15 1.00 0.15 0.15
8 0.19 0.18 0.16 0.18 0.17 0.16 0.15 1.00 0.19
9 0.17 0.19 0.16 0.18 0.17 0.17 0.15 0.19 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