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Status: Done started: 2014-May-22 20:40:53 UTC
Project NameT248
SequenceGYDNREIVMKYIHYKLSQRGYEWDAGDDVEENRTEAPEGTESEVVHLTLRQAGDDFSRRYRRDFAEMSSQLHLTPFTARG RFATVVEELFRDGVNWGRIVAFFEFGGVMCVESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGP
Secondary structure

CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCHHHHHHHHCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2014-May-23 10:35 UTC

Provided templates.

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

Cluster #123456789
Cluster density65.254.432.632.426.021.818.117.316.0
Cluster size686433474131272722
Average cluster RMSD1.01.21.01.51.61.41.51.61.4

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 1.06 1.66 1.82 1.45 1.65 2.29 2.26 2.40
2 1.06 0.00 1.64 1.54 1.43 1.51 1.83 1.92 2.12
3 1.66 1.64 0.00 1.79 1.41 1.91 2.24 2.19 2.27
4 1.82 1.54 1.79 0.00 1.41 1.38 1.61 1.73 1.57
5 1.45 1.43 1.41 1.41 0.00 1.35 1.85 1.77 2.11
6 1.65 1.51 1.91 1.38 1.35 0.00 1.71 1.46 1.87
7 2.29 1.83 2.24 1.61 1.85 1.71 0.00 1.68 1.54
8 2.26 1.92 2.19 1.73 1.77 1.46 1.68 0.00 1.97
9 2.40 2.12 2.27 1.57 2.11 1.87 1.54 1.97 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 0.95 0.93 0.92 0.92 0.93 0.92 0.91 0.92
2 0.95 1.00 0.92 0.92 0.92 0.92 0.94 0.94 0.93
3 0.93 0.92 1.00 0.91 0.92 0.92 0.90 0.90 0.91
4 0.92 0.92 0.91 1.00 0.93 0.93 0.94 0.92 0.93
5 0.92 0.92 0.92 0.93 1.00 0.94 0.92 0.93 0.91
6 0.93 0.92 0.92 0.93 0.94 1.00 0.94 0.94 0.93
7 0.92 0.94 0.90 0.94 0.92 0.94 1.00 0.94 0.94
8 0.91 0.94 0.90 0.92 0.93 0.94 0.94 1.00 0.92
9 0.92 0.93 0.91 0.93 0.91 0.93 0.94 0.92 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