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Status: Done started: 2017-Aug-28 19:50:15 UTC
Project Namersu1
SequenceSMLDINGLF
Secondary structure

CCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Aug-29 00:11 UTC

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

Cluster #123456789
Cluster density120.927.623.820.416.914.113.69.97.7
Cluster size1234242413228212011
Average cluster RMSD1.01.51.82.01.92.01.52.01.4

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 3.32 3.87 3.17 2.70 2.68 3.30 2.48 4.24
2 3.32 0.00 2.54 3.09 2.28 1.95 2.18 3.79 4.31
3 3.87 2.54 0.00 2.36 2.88 3.17 3.73 3.75 4.95
4 3.17 3.09 2.36 0.00 3.23 2.73 3.89 2.42 4.96
5 2.70 2.28 2.88 3.23 0.00 2.32 2.29 3.04 3.36
6 2.68 1.95 3.17 2.73 2.32 0.00 2.29 2.88 4.11
7 3.30 2.18 3.73 3.89 2.29 2.29 0.00 3.30 2.76
8 2.48 3.79 3.75 2.42 3.04 2.88 3.30 0.00 3.28
9 4.24 4.31 4.95 4.96 3.36 4.11 2.76 3.28 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 0.64 0.72 0.64 0.75 0.64 0.75 0.50
2 0.67 1.00 0.69 0.64 0.72 0.86 0.78 0.53 0.69
3 0.64 0.69 1.00 0.56 0.72 0.58 0.67 0.50 0.67
4 0.72 0.64 0.56 1.00 0.50 0.64 0.53 0.81 0.44
5 0.64 0.72 0.72 0.50 1.00 0.67 0.69 0.56 0.72
6 0.75 0.86 0.58 0.64 0.67 1.00 0.81 0.75 0.61
7 0.64 0.78 0.67 0.53 0.69 0.81 1.00 0.67 0.78
8 0.75 0.53 0.50 0.81 0.56 0.75 0.67 1.00 0.58
9 0.50 0.69 0.67 0.44 0.72 0.61 0.78 0.58 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