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Status: Done started: 2020-Apr-12 22:41:22 UTC
Project NameAVP1632
SequencePGDPDLSDGSWSTVSSGA
Secondary structure

CCCCCCCCCCEEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-13 03:47 UTC

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

Cluster #123456789
Cluster density21.620.117.415.514.410.39.08.98.1
Cluster size456258434129262828
Average cluster RMSD2.13.13.32.82.82.82.93.23.5

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 7.86 4.71 4.69 7.05 9.69 12.20 9.96 7.07
2 7.86 0.00 4.36 5.54 3.66 3.64 5.34 3.95 4.21
3 4.71 4.36 0.00 3.59 4.06 6.01 8.34 6.48 4.34
4 4.69 5.54 3.59 0.00 3.99 6.54 9.33 7.92 6.63
5 7.05 3.66 4.06 3.99 0.00 4.22 6.57 5.03 5.24
6 9.69 3.64 6.01 6.54 4.22 0.00 3.86 3.71 5.24
7 12.20 5.34 8.34 9.33 6.57 3.86 0.00 3.12 6.09
8 9.96 3.95 6.48 7.92 5.03 3.71 3.12 0.00 4.04
9 7.07 4.21 4.34 6.63 5.24 5.24 6.09 4.04 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 0.46 0.53 0.56 0.47 0.46 0.46 0.47 0.49
2 0.46 1.00 0.56 0.51 0.61 0.56 0.50 0.54 0.51
3 0.53 0.56 1.00 0.57 0.53 0.49 0.47 0.50 0.56
4 0.56 0.51 0.57 1.00 0.61 0.60 0.57 0.53 0.49
5 0.47 0.61 0.53 0.61 1.00 0.62 0.56 0.65 0.46
6 0.46 0.56 0.49 0.60 0.62 1.00 0.68 0.58 0.49
7 0.46 0.50 0.47 0.57 0.56 0.68 1.00 0.64 0.56
8 0.47 0.54 0.50 0.53 0.65 0.58 0.64 1.00 0.65
9 0.49 0.51 0.56 0.49 0.46 0.49 0.56 0.65 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