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Status: Done started: 2015-Jun-06 04:51:30 UTC
Project Name3
SequenceQTFANLWRLLAQN
Secondary structure

CHHHHHHHHHHCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Jun-06 09:15 UTC

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

Cluster #123456789
Cluster density166.994.756.454.931.614.89.65.45.2
Cluster size107695648331813106
Average cluster RMSD0.60.71.00.91.01.21.31.81.1

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 0.46 0.62 0.32 0.72 1.99 1.58 1.97 2.03
2 0.46 0.00 0.52 0.50 0.65 1.84 1.42 2.19 2.01
3 0.62 0.52 0.00 0.64 1.10 1.79 1.60 2.44 2.33
4 0.32 0.50 0.64 0.00 0.73 1.98 1.56 1.93 2.01
5 0.72 0.65 1.10 0.73 0.00 1.92 1.25 1.79 1.59
6 1.99 1.84 1.79 1.98 1.92 0.00 1.46 2.52 2.48
7 1.58 1.42 1.60 1.56 1.25 1.46 0.00 1.97 1.46
8 1.97 2.19 2.44 1.93 1.79 2.52 1.97 0.00 1.82
9 2.03 2.01 2.33 2.01 1.59 2.48 1.46 1.82 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 0.98 0.98 1.00 0.96 0.94 0.92 0.85 0.90
2 0.98 1.00 0.98 0.98 0.98 0.94 0.90 0.83 0.90
3 0.98 0.98 1.00 0.96 0.94 0.94 0.90 0.83 0.90
4 1.00 0.98 0.96 1.00 0.96 0.94 0.92 0.85 0.90
5 0.96 0.98 0.94 0.96 1.00 0.94 0.92 0.88 0.92
6 0.94 0.94 0.94 0.94 0.94 1.00 0.92 0.85 0.90
7 0.92 0.90 0.90 0.92 0.92 0.92 1.00 0.86 0.92
8 0.85 0.83 0.83 0.85 0.88 0.85 0.86 1.00 0.85
9 0.90 0.90 0.90 0.90 0.92 0.90 0.92 0.85 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