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Status: Done started: 2020-Jan-06 18:41:49 UTC
Project NameMLP22-PT72
SequenceASEGGPDPHNCL
Secondary structure

CCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Jan-06 22:08 UTC

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

Cluster #123456789
Cluster density30.220.318.915.915.515.014.914.511.7
Cluster size824346333834312528
Average cluster RMSD2.72.12.42.12.42.32.11.72.4

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 4.15 3.42 3.63 4.10 3.95 4.59 5.63 4.26
2 4.15 0.00 3.75 2.82 4.30 2.67 3.12 2.90 3.42
3 3.42 3.75 0.00 2.25 3.20 3.26 3.63 4.56 2.91
4 3.63 2.82 2.25 0.00 3.84 2.72 3.50 4.02 2.56
5 4.10 4.30 3.20 3.84 0.00 3.03 3.87 4.95 3.69
6 3.95 2.67 3.26 2.72 3.03 0.00 2.44 3.59 2.76
7 4.59 3.12 3.63 3.50 3.87 2.44 0.00 3.10 3.10
8 5.63 2.90 4.56 4.02 4.95 3.59 3.10 0.00 3.95
9 4.26 3.42 2.91 2.56 3.69 2.76 3.10 3.95 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 0.58 0.67 0.60 0.62 0.48 0.50 0.44 0.52
2 0.58 1.00 0.58 0.69 0.54 0.67 0.67 0.69 0.58
3 0.67 0.58 1.00 0.75 0.67 0.65 0.65 0.62 0.67
4 0.60 0.69 0.75 1.00 0.58 0.71 0.67 0.60 0.71
5 0.62 0.54 0.67 0.58 1.00 0.67 0.62 0.60 0.65
6 0.48 0.67 0.65 0.71 0.67 1.00 0.60 0.60 0.60
7 0.50 0.67 0.65 0.67 0.62 0.60 1.00 0.77 0.69
8 0.44 0.69 0.62 0.60 0.60 0.60 0.77 1.00 0.67
9 0.52 0.58 0.67 0.71 0.65 0.60 0.69 0.67 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