Download models Download trajectory View trajectory
Status: Done started: 2018-Mar-17 19:31:58 UTC
Project NameSericinAlligned
SequenceDPNGGSASAGQSRDSSLRERNVHYV
Secondary structure

CCCCCCCCCCCCCCCHHHHHCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Mar-17 23:39 UTC

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

Cluster #123456789
Cluster density48.914.511.38.37.67.46.44.73.0
Cluster size1185147302931261810
Average cluster RMSD2.43.54.23.63.84.24.13.93.3

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 2.16 7.06 5.78 5.60 7.81 5.91 6.86 5.10
2 2.16 0.00 7.21 5.04 5.16 7.40 5.35 6.24 4.41
3 7.06 7.21 0.00 8.78 6.63 3.68 5.97 6.97 9.27
4 5.78 5.04 8.78 0.00 5.24 8.97 5.15 6.55 4.47
5 5.60 5.16 6.63 5.24 0.00 7.33 5.16 7.60 7.25
6 7.81 7.40 3.68 8.97 7.33 0.00 5.99 6.41 9.18
7 5.91 5.35 5.97 5.15 5.16 5.99 0.00 4.97 6.58
8 6.86 6.24 6.97 6.55 7.60 6.41 4.97 0.00 6.00
9 5.10 4.41 9.27 4.47 7.25 9.18 6.58 6.00 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 0.89 0.51 0.43 0.52 0.55 0.43 0.41 0.58
2 0.89 1.00 0.53 0.49 0.54 0.56 0.44 0.44 0.62
3 0.51 0.53 1.00 0.45 0.59 0.62 0.49 0.44 0.47
4 0.43 0.49 0.45 1.00 0.52 0.47 0.51 0.45 0.52
5 0.52 0.54 0.59 0.52 1.00 0.56 0.54 0.48 0.54
6 0.55 0.56 0.62 0.47 0.56 1.00 0.48 0.44 0.49
7 0.43 0.44 0.49 0.51 0.54 0.48 1.00 0.52 0.47
8 0.41 0.44 0.44 0.45 0.48 0.44 0.52 1.00 0.50
9 0.58 0.62 0.47 0.52 0.54 0.49 0.47 0.50 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