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Status: Done started: 2014-Sep-22 12:38:50 UTC
Project NameHcpR_fold
SequenceLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVGVGEIRAEMVGPSGKQILIDTLAVGRIL APALLFASENILPVTLFANEDSVLFRIGKEEFKGMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQL YTKDGSNRIVVESSWKELSDRFGVNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRLE
Secondary structure

CHHHHCCCHHHHCCCHHHHHHHHCCCCCCEEECCCCEEEECCCCCCCEEEEEEECCEECCCCCCCCCCCCCCEECCCEEE CCCCCCCCCCCCCCCEEECCCCEEEEEECHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHCCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHCCEEECCCCEEECCCCCCCCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2014-Sep-23 02:33 UTC

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

Cluster #123456789
Cluster density42.622.121.312.811.28.87.41.41.0
Cluster size87703046414226108
Average cluster RMSD2.03.21.43.63.74.73.56.98.1

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 22.70 21.30 4.18 18.30 17.80 18.80 18.50 21.80
2 22.70 0.00 20.30 23.70 25.40 22.30 18.60 18.60 22.60
3 21.30 20.30 0.00 22.10 22.10 17.40 19.80 21.40 16.60
4 4.18 23.70 22.10 0.00 18.20 18.20 19.00 19.00 21.50
5 18.30 25.40 22.10 18.20 0.00 17.20 19.00 18.30 17.90
6 17.80 22.30 17.40 18.20 17.20 0.00 19.40 17.10 16.90
7 18.80 18.60 19.80 19.00 19.00 19.40 0.00 15.60 19.90
8 18.50 18.60 21.40 19.00 18.30 17.10 15.60 0.00 20.40
9 21.80 22.60 16.60 21.50 17.90 16.90 19.90 20.40 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 0.17 0.14 0.52 0.16 0.16 0.13 0.14 0.15
2 0.17 1.00 0.13 0.15 0.12 0.12 0.13 0.13 0.12
3 0.14 0.13 1.00 0.16 0.12 0.16 0.14 0.15 0.14
4 0.52 0.15 0.16 1.00 0.17 0.16 0.14 0.16 0.15
5 0.16 0.12 0.12 0.17 1.00 0.16 0.13 0.14 0.22
6 0.16 0.12 0.16 0.16 0.16 1.00 0.15 0.13 0.18
7 0.13 0.13 0.14 0.14 0.13 0.15 1.00 0.15 0.13
8 0.14 0.13 0.15 0.16 0.14 0.13 0.15 1.00 0.14
9 0.15 0.12 0.14 0.15 0.22 0.18 0.13 0.14 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.


 

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