Download models Download trajectory View trajectory
Status: Done started: 2015-Apr-23 07:37:19 UTC
Project Namenatalp3
SequenceMEAVDANSLAQAKEAAIKELKQYGIGDYYIKLINNAKTVEGVESLKNEILKALPTE
Secondary structure

CHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Apr-23 14:38 UTC

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

Cluster #123
Cluster density67.242.64.0
Cluster size17816418
Average cluster RMSD2.63.84.5

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.

#123
1 0.00 18.70 9.95
2 18.70 0.00 11.00
3 9.95 11.00 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.

#123
1 1.00 0.56 0.48
2 0.56 1.00 0.50
3 0.48 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