Download models Download trajectory View trajectory
Status: Done started: 2020-Apr-14 03:59:22 UTC
Project NameAVP1787
SequenceYQFHLVLHEALRAQALSRQLILGRELAQELVAELAT
Secondary structure

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-14 10:48 UTC

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

Cluster #123456789
Cluster density78.761.523.319.616.815.614.713.77.4
Cluster size977335352623292814
Average cluster RMSD1.21.21.51.81.51.52.02.01.9

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 0.65 0.51 1.15 1.18 0.89 0.94 1.03 3.20
2 0.65 0.00 0.39 0.83 0.89 0.60 0.78 1.07 3.18
3 0.51 0.39 0.00 0.92 0.83 0.56 0.83 0.85 3.12
4 1.15 0.83 0.92 0.00 1.20 0.93 0.57 1.09 3.15
5 1.18 0.89 0.83 1.20 0.00 0.93 1.27 1.15 3.13
6 0.89 0.60 0.56 0.93 0.93 0.00 0.88 0.93 3.04
7 0.94 0.78 0.83 0.57 1.27 0.88 0.00 1.05 3.09
8 1.03 1.07 0.85 1.09 1.15 0.93 1.05 0.00 2.91
9 3.20 3.18 3.12 3.15 3.13 3.04 3.09 2.91 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 0.97 0.99 0.93 0.96 0.96 0.94 0.95 0.76
2 0.97 1.00 0.99 0.97 0.97 0.98 0.96 0.93 0.77
3 0.99 0.99 1.00 0.96 0.98 0.99 0.96 0.97 0.77
4 0.93 0.97 0.96 1.00 0.94 0.94 0.99 0.94 0.78
5 0.96 0.97 0.98 0.94 1.00 0.96 0.94 0.94 0.76
6 0.96 0.98 0.99 0.94 0.96 1.00 0.96 0.97 0.77
7 0.94 0.96 0.96 0.99 0.94 0.96 1.00 0.95 0.78
8 0.95 0.93 0.97 0.94 0.94 0.97 0.95 1.00 0.77
9 0.76 0.77 0.77 0.78 0.76 0.77 0.78 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