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Status: Done started: 2020-Sep-03 17:31:35 UTC
Project Name1BH4_KW_sec_ssbonds
SequenceCGESCVWIPCISAALGCSCKNKVCYRNGIP
Secondary structure

CCCCCCCCCCCHHHHCCCCCCCCCCCCCCC

User provided constraintsYes
Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Sep-04 00:40 UTC

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

Cluster #123456789
Cluster density17.116.213.611.910.810.69.17.66.7
Cluster size474647484032373429
Average cluster RMSD2.82.83.54.03.73.04.14.54.3

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 3.74 3.90 2.33 2.52 4.51 5.73 6.59 4.78
2 3.74 0.00 3.20 4.35 4.14 3.35 4.86 6.80 5.32
3 3.90 3.20 0.00 3.67 4.49 1.96 5.66 6.83 4.22
4 2.33 4.35 3.67 0.00 2.52 4.15 5.54 6.89 4.39
5 2.52 4.14 4.49 2.52 0.00 4.90 5.05 7.39 5.43
6 4.51 3.35 1.96 4.15 4.90 0.00 6.13 7.10 4.30
7 5.73 4.86 5.66 5.54 5.05 6.13 0.00 6.80 7.66
8 6.59 6.80 6.83 6.89 7.39 7.10 6.80 0.00 4.59
9 4.78 5.32 4.22 4.39 5.43 4.30 7.66 4.59 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 0.60 0.59 0.73 0.70 0.53 0.48 0.58 0.60
2 0.60 1.00 0.66 0.57 0.64 0.71 0.52 0.50 0.56
3 0.59 0.66 1.00 0.72 0.57 0.80 0.49 0.48 0.65
4 0.73 0.57 0.72 1.00 0.72 0.64 0.55 0.49 0.62
5 0.70 0.64 0.57 0.72 1.00 0.56 0.59 0.51 0.56
6 0.53 0.71 0.80 0.64 0.56 1.00 0.51 0.47 0.68
7 0.48 0.52 0.49 0.55 0.59 0.51 1.00 0.49 0.46
8 0.58 0.50 0.48 0.49 0.51 0.47 0.49 1.00 0.58
9 0.60 0.56 0.65 0.62 0.56 0.68 0.46 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