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Status: Done started: 2017-Dec-02 12:43:07 UTC
Project Name1
SequenceMAPQSITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGATFQVEVPGSQHIDSQKKAIERMKDTLRITYLTE TKIDKLCVWNNKTPNSIAAISMENYAPQDPYAPQDPIVVTGDKAVNIYTSSQTGSIIVKLLPNLPKDKEACAKAPLDAYN RTLTTLLTPLGDSIRRIQESVTTSGGGRQGRLIGAIIGGVALGVATPAQITAAAALIQAKQNAANILRLKESIAATNEAV HEVTDGLSQLAVAVGKMYAPQDPYAPQDPVANYPGVGGGSFIDSRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPD EQDYQIRMAKSSYKPGRFGGSEKDELHHHHHH
Secondary structure

CCCHHHHHHHHHHCCCEEEEECCCCCHHCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCHHHHHHHHHHCCEEEEEEEC CCCCCCCHHHHHHHHHHHCEECCCCCCCCCCCCCCCEEEECCEEEEEEECCCCCCEEEECCCCCCCCHHHHHCCCHHHHH HHHHHHCCCCHHHHHHHCCCEECCCCCCCCCEEEEEEEHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCC CCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2017-Dec-03 01:38 UTC

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

Cluster #12345678
Cluster density33.026.010.55.94.84.13.41.5
Cluster size10410462222521157
Average cluster RMSD3.24.05.93.85.35.14.54.8

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 26.10 25.30 26.80 34.00 23.40 37.40 33.70
2 26.10 0.00 10.90 24.90 30.10 23.80 33.20 30.60
3 25.30 10.90 0.00 25.50 29.80 23.20 32.10 31.60
4 26.80 24.90 25.50 0.00 32.70 28.70 35.90 32.70
5 34.00 30.10 29.80 32.70 0.00 28.80 12.30 11.20
6 23.40 23.80 23.20 28.70 28.80 0.00 31.20 30.50
7 37.40 33.20 32.10 35.90 12.30 31.20 0.00 14.70
8 33.70 30.60 31.60 32.70 11.20 30.50 14.70 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.

#12345678
1 1.00 0.13 0.12 0.12 0.12 0.11 0.12 0.10
2 0.13 1.00 0.39 0.12 0.13 0.11 0.12 0.11
3 0.12 0.39 1.00 0.10 0.10 0.09 0.09 0.09
4 0.12 0.12 0.10 1.00 0.10 0.10 0.11 0.10
5 0.12 0.13 0.10 0.10 1.00 0.11 0.32 0.35
6 0.11 0.11 0.09 0.10 0.11 1.00 0.10 0.11
7 0.12 0.12 0.09 0.11 0.32 0.10 1.00 0.29
8 0.10 0.11 0.09 0.10 0.35 0.11 0.29 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