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Status: Done started: 2015-Dec-05 15:02:46 UTC
Project NameArabidopsis_C
SequenceYGDKFMDEYQAIMSKKLGLTKYNKEVISKLLNNMSVDKVDYTNFFRLLANVKANPNTPENELLKPLKAVLLDIGKERKEA WIKWMRSYIQEVGGSEVSDEERKARMDSVNPKYILRNYLCQSAIDAAEQGDFSEVNNLIRLMKRPYEEQPGMEKYARLPP AWAYRPGVCMLSCSS
Secondary structure

CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Dec-06 03:57 UTC

Provided templates.

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

Cluster #12345678
Cluster density127.3106.1103.784.050.949.247.443.9
Cluster size7661605032303120
Average cluster RMSD0.60.60.60.60.60.60.70.5

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.

#12345678
1 0.00 0.94 0.79 1.00 1.18 0.83 0.79 0.85
2 0.94 0.00 0.97 0.64 1.04 0.86 0.77 0.92
3 0.79 0.97 0.00 0.94 1.33 0.86 0.68 0.80
4 1.00 0.64 0.94 0.00 1.08 0.87 0.73 0.93
5 1.18 1.04 1.33 1.08 0.00 1.24 1.24 1.34
6 0.83 0.86 0.86 0.87 1.24 0.00 0.72 0.84
7 0.79 0.77 0.68 0.73 1.24 0.72 0.00 0.79
8 0.85 0.92 0.80 0.93 1.34 0.84 0.79 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 0.96 0.97 0.96 0.95 0.97 0.97 0.97
2 0.96 1.00 0.97 0.98 0.95 0.96 0.97 0.96
3 0.97 0.97 1.00 0.97 0.95 0.96 0.99 0.96
4 0.96 0.98 0.97 1.00 0.96 0.96 0.98 0.95
5 0.95 0.95 0.95 0.96 1.00 0.94 0.96 0.93
6 0.97 0.96 0.96 0.96 0.94 1.00 0.97 0.96
7 0.97 0.97 0.99 0.98 0.96 0.97 1.00 0.97
8 0.97 0.96 0.96 0.95 0.93 0.96 0.97 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