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Status: Done started: 2015-Apr-09 08:32:02 UTC
Project Namene1nh
SequenceDGVLSGEELHELFHTIDTHNTNNLDTEELCEYFSQHLGEYENVLAALEDLNLSILKAMGKTKKDYQEASNLEQFVTRFLL KETLNQLQSLQNSLECAMETTEEQTRQERQGPAKPE
Secondary structure

CCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC

Simulation (CABS) temperature2.5 - 1.0
Estimated finish time2015-Apr-09 20:05 UTC

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

Cluster #123456789
Cluster density64.754.850.343.542.733.824.721.621.5
Cluster size655249463935262523
Average cluster RMSD1.00.91.01.10.91.01.11.21.1

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 1.24 0.96 1.55 1.80 1.22 1.30 1.40 0.93
2 1.24 0.00 0.93 1.08 0.95 1.08 0.63 1.92 0.83
3 0.96 0.93 0.00 1.16 1.41 0.87 1.08 1.61 0.81
4 1.55 1.08 1.16 0.00 1.14 0.94 0.87 2.25 1.18
5 1.80 0.95 1.41 1.14 0.00 1.45 0.81 2.66 1.49
6 1.22 1.08 0.87 0.94 1.45 0.00 0.99 1.73 0.94
7 1.30 0.63 1.08 0.87 0.81 0.99 0.00 2.14 0.97
8 1.40 1.92 1.61 2.25 2.66 1.73 2.14 0.00 1.39
9 0.93 0.83 0.81 1.18 1.49 0.94 0.97 1.39 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 0.92 0.96 0.87 0.85 0.92 0.90 0.91 0.96
2 0.92 1.00 0.96 0.94 0.94 0.93 0.99 0.84 0.96
3 0.96 0.96 1.00 0.92 0.88 0.96 0.94 0.87 0.97
4 0.87 0.94 0.92 1.00 0.92 0.96 0.96 0.81 0.91
5 0.85 0.94 0.88 0.92 1.00 0.88 0.95 0.78 0.89
6 0.92 0.93 0.96 0.96 0.88 1.00 0.94 0.86 0.94
7 0.90 0.99 0.94 0.96 0.95 0.94 1.00 0.80 0.94
8 0.91 0.84 0.87 0.81 0.78 0.86 0.80 1.00 0.89
9 0.96 0.96 0.97 0.91 0.89 0.94 0.94 0.89 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