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Status: Done started: 2020-Apr-13 00:33:26 UTC
Project NameAVP1633
SequenceFYHSKRRLIFSKRKP
Secondary structure

CCCCCEEEEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-13 05:21 UTC

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

Cluster #123456789
Cluster density32.831.724.318.116.010.38.88.45.4
Cluster size667261444024182114
Average cluster RMSD2.02.32.52.42.52.32.12.52.6

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 3.02 3.28 1.96 3.01 5.53 6.88 4.86 7.47
2 3.02 0.00 2.55 3.79 3.89 3.46 5.00 3.51 5.74
3 3.28 2.55 0.00 2.97 3.09 4.08 5.69 3.51 5.83
4 1.96 3.79 2.97 0.00 2.77 5.94 7.37 5.24 7.65
5 3.01 3.89 3.09 2.77 0.00 5.76 7.20 4.44 6.97
6 5.53 3.46 4.08 5.94 5.76 0.00 2.98 3.03 3.58
7 6.88 5.00 5.69 7.37 7.20 2.98 0.00 3.89 3.20
8 4.86 3.51 3.51 5.24 4.44 3.03 3.89 0.00 3.88
9 7.47 5.74 5.83 7.65 6.97 3.58 3.20 3.88 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 0.67 0.60 0.83 0.72 0.67 0.65 0.57 0.62
2 0.67 1.00 0.73 0.63 0.65 0.72 0.68 0.65 0.58
3 0.60 0.73 1.00 0.63 0.63 0.58 0.57 0.62 0.63
4 0.83 0.63 0.63 1.00 0.72 0.63 0.55 0.58 0.57
5 0.72 0.65 0.63 0.72 1.00 0.58 0.55 0.63 0.63
6 0.67 0.72 0.58 0.63 0.58 1.00 0.72 0.70 0.67
7 0.65 0.68 0.57 0.55 0.55 0.72 1.00 0.65 0.68
8 0.57 0.65 0.62 0.58 0.63 0.70 0.65 1.00 0.72
9 0.62 0.58 0.63 0.57 0.63 0.67 0.68 0.72 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