Download models Download trajectory View trajectory
Status: Done started: 2017-Jul-08 20:07:57 UTC
Project Namechi040717
SequenceNSTTFHQALLDPRVRGLYFPAGG
Secondary structure

CHHHHHHHHHCCEEEEEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Jul-09 01:46 UTC

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

Cluster #12345678
Cluster density34.830.523.614.07.97.46.56.3
Cluster size8773674726211920
Average cluster RMSD2.52.42.83.43.32.82.93.2

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.

#12345678
1 0.00 2.89 4.13 3.59 5.92 5.99 9.22 8.76
2 2.89 0.00 4.36 4.12 4.64 4.19 7.43 7.29
3 4.13 4.36 0.00 3.93 4.13 6.36 8.51 7.90
4 3.59 4.12 3.93 0.00 5.60 6.01 9.02 8.40
5 5.92 4.64 4.13 5.60 0.00 4.14 5.25 5.22
6 5.99 4.19 6.36 6.01 4.14 0.00 4.72 4.89
7 9.22 7.43 8.51 9.02 5.25 4.72 0.00 3.71
8 8.76 7.29 7.90 8.40 5.22 4.89 3.71 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.

#12345678
1 1.00 0.78 0.64 0.67 0.58 0.66 0.49 0.52
2 0.78 1.00 0.62 0.73 0.62 0.68 0.51 0.53
3 0.64 0.62 1.00 0.67 0.69 0.56 0.53 0.51
4 0.67 0.73 0.67 1.00 0.60 0.63 0.51 0.52
5 0.58 0.62 0.69 0.60 1.00 0.62 0.53 0.51
6 0.66 0.68 0.56 0.63 0.62 1.00 0.60 0.56
7 0.49 0.51 0.53 0.51 0.53 0.60 1.00 0.64
8 0.52 0.53 0.51 0.52 0.51 0.56 0.64 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