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Status: Done started: 2016-Mar-14 10:17:19 UTC
Project Nameron2main6riya
SequenceYGNEKNPNIFPGSPRNINVYSVHHIPNNGANGGLNSGANGGLNNGANDGLNNGANGGLNNGANGGLNNGANGGLNNGMNN GMNNGMNNGMNNGMNNGMNNGMNNGTNGGLN
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2016-Mar-14 23:12 UTC

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

Cluster #123456789
Cluster density11.94.13.42.41.91.71.21.10.9
Cluster size1086352342927171614
Average cluster RMSD9.115.215.114.315.315.713.715.214.7

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 21.50 15.60 19.30 19.10 21.60 23.90 24.20 23.40
2 21.50 0.00 18.80 17.30 23.30 20.40 17.70 19.40 23.10
3 15.60 18.80 0.00 21.10 21.40 21.10 20.00 20.40 20.60
4 19.30 17.30 21.10 0.00 19.90 20.30 18.60 22.70 25.70
5 19.10 23.30 21.40 19.90 0.00 17.30 23.70 20.50 22.10
6 21.60 20.40 21.10 20.30 17.30 0.00 21.30 20.60 23.10
7 23.90 17.70 20.00 18.60 23.70 21.30 0.00 17.50 24.50
8 24.20 19.40 20.40 22.70 20.50 20.60 17.50 0.00 20.70
9 23.40 23.10 20.60 25.70 22.10 23.10 24.50 20.70 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 0.14 0.13 0.12 0.14 0.11 0.12 0.11 0.15
2 0.14 1.00 0.14 0.13 0.13 0.15 0.13 0.15 0.14
3 0.13 0.14 1.00 0.14 0.11 0.13 0.12 0.15 0.13
4 0.12 0.13 0.14 1.00 0.12 0.12 0.15 0.14 0.13
5 0.14 0.13 0.11 0.12 1.00 0.15 0.11 0.14 0.10
6 0.11 0.15 0.13 0.12 0.15 1.00 0.13 0.16 0.11
7 0.12 0.13 0.12 0.15 0.11 0.13 1.00 0.13 0.13
8 0.11 0.15 0.15 0.14 0.14 0.16 0.13 1.00 0.13
9 0.15 0.14 0.13 0.13 0.10 0.11 0.13 0.13 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