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Status: Done started: 2015-Jan-30 17:48:58 UTC
Project Namenpy1-36
SequenceYPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY
Secondary structure

CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Jan-30 22:33 UTC

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

Cluster #12345678
Cluster density32.314.011.911.511.09.59.38.2
Cluster size9547434045333126
Average cluster RMSD2.93.43.63.54.13.53.33.2

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.

#12345678
1 0.00 6.86 3.97 4.11 9.38 4.25 3.07 3.06
2 6.86 0.00 7.47 4.13 4.20 5.67 8.10 8.51
3 3.97 7.47 0.00 5.36 9.65 3.86 3.74 4.88
4 4.11 4.13 5.36 0.00 6.89 4.00 5.05 5.48
5 9.38 4.20 9.65 6.89 0.00 7.84 10.90 11.00
6 4.25 5.67 3.86 4.00 7.84 0.00 4.44 6.20
7 3.07 8.10 3.74 5.05 10.90 4.44 0.00 3.34
8 3.06 8.51 4.88 5.48 11.00 6.20 3.34 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.

#12345678
1 1.00 0.67 0.69 0.75 0.63 0.74 0.73 0.80
2 0.67 1.00 0.65 0.73 0.70 0.68 0.68 0.69
3 0.69 0.65 1.00 0.73 0.60 0.81 0.78 0.69
4 0.75 0.73 0.73 1.00 0.65 0.73 0.74 0.83
5 0.63 0.70 0.60 0.65 1.00 0.60 0.63 0.65
6 0.74 0.68 0.81 0.73 0.60 1.00 0.75 0.71
7 0.73 0.68 0.78 0.74 0.63 0.75 1.00 0.77
8 0.80 0.69 0.69 0.83 0.65 0.71 0.77 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