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Status: Done started: 2013-Oct-28 21:00:07 UTC
Project Namewwwwdenovo
SequenceVVPQYGGGGGNHGGGGNNSGPNSELNIYQYGGGNSALALQTDARNSDLTITQHGGGNGADVGQGSDDSSIDLTQRGFGNS ATLDQWNGKNSEMTVKQFGGGNGAAVDQTASNSSVNVTQVGFGNNATAHQY
Secondary structure

CEEECCCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEEECCCCCEEEEEEECCCCEEEEEECCCCCEEEEEEECCCCE EEEEEECCCCCEEEEEEECCCCCEEEEEECCCCEEEEEEECCCCEEEEEEC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2013-Oct-29 09:55 UTC

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

Cluster #123456789
Cluster density24.92.92.01.61.41.00.80.60.5
Cluster size187373527251714108
Average cluster RMSD7.512.617.217.118.216.416.816.914.9

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 18.10 19.50 20.60 21.90 21.00 19.80 24.10 24.40
2 18.10 0.00 21.00 22.70 23.60 21.00 27.20 22.70 23.70
3 19.50 21.00 0.00 22.70 21.20 22.10 22.80 27.40 24.00
4 20.60 22.70 22.70 0.00 24.50 25.30 22.70 28.80 25.70
5 21.90 23.60 21.20 24.50 0.00 22.30 26.80 25.20 26.20
6 21.00 21.00 22.10 25.30 22.30 0.00 23.60 19.40 19.40
7 19.80 27.20 22.80 22.70 26.80 23.60 0.00 26.50 26.90
8 24.10 22.70 27.40 28.80 25.20 19.40 26.50 0.00 19.20
9 24.40 23.70 24.00 25.70 26.20 19.40 26.90 19.20 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 0.10 0.11 0.11 0.12 0.12 0.11 0.10
2 0.17 1.00 0.13 0.14 0.10 0.11 0.11 0.10 0.11
3 0.10 0.13 1.00 0.11 0.13 0.11 0.12 0.11 0.12
4 0.11 0.14 0.11 1.00 0.14 0.11 0.10 0.09 0.12
5 0.11 0.10 0.13 0.14 1.00 0.12 0.11 0.10 0.12
6 0.12 0.11 0.11 0.11 0.12 1.00 0.11 0.10 0.12
7 0.12 0.11 0.12 0.10 0.11 0.11 1.00 0.10 0.12
8 0.11 0.10 0.11 0.09 0.10 0.10 0.10 1.00 0.11
9 0.10 0.11 0.12 0.12 0.12 0.12 0.12 0.11 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