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Status: Done started: 2015-Oct-29 02:46:27 UTC
Project Namenad6_ref
SequenceMMYALFLLSVGLVMGFVGFSSKPSPIYGGLVLIVSGVVGCVIILNFGGGYMGLMVFLIYLGGMMVVFGYTTAMAIEEYPE AWGSGVEVLVSVLVGLAMEVGLVLWVKEYDGVVVVVNFNSVGSWMIYEGEGSGLIREDPIGAGALYDYGRWLVVVTGWTL FVGVYIVIEIARGN
Secondary structure

CEEHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCEEEEEEEECCCCCHHHHHHHHHHCCEEEEECCHHHHHCCCCCC CCCCCCHHHHHHHHHHHHHHHEEEEEEECCEEEEEEEECCCCCEEEEECCCEEEEECCCEEEEEEECCCEEEEEEEEEEE EEEEEEEEEEECCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Oct-29 15:41 UTC

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

Cluster #12345678910
Cluster density37.118.811.57.75.23.62.42.42.31.7
Cluster size90722324193622282620
Average cluster RMSD2.43.82.03.13.710.09.211.911.211.7

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.

#12345678910
1 0.00 15.50 16.90 17.60 19.60 19.90 19.10 17.20 18.50 18.50
2 15.50 0.00 16.60 18.70 18.70 16.60 18.70 16.70 20.00 16.70
3 16.90 16.60 0.00 17.60 19.50 18.40 18.20 18.40 17.80 17.50
4 17.60 18.70 17.60 0.00 18.10 16.30 16.70 19.00 15.70 19.60
5 19.60 18.70 19.50 18.10 0.00 14.60 16.70 18.60 15.20 17.90
6 19.90 16.60 18.40 16.30 14.60 0.00 18.90 16.20 12.30 19.70
7 19.10 18.70 18.20 16.70 16.70 18.90 0.00 18.10 18.50 17.70
8 17.20 16.70 18.40 19.00 18.60 16.20 18.10 0.00 19.10 17.00
9 18.50 20.00 17.80 15.70 15.20 12.30 18.50 19.10 0.00 20.30
10 18.50 16.70 17.50 19.60 17.90 19.70 17.70 17.00 20.30 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.

#12345678910
1 1.00 0.16 0.17 0.18 0.23 0.12 0.13 0.16 0.13 0.16
2 0.16 1.00 0.22 0.14 0.15 0.15 0.15 0.17 0.12 0.15
3 0.17 0.22 1.00 0.20 0.18 0.14 0.13 0.16 0.14 0.17
4 0.18 0.14 0.20 1.00 0.17 0.17 0.15 0.17 0.16 0.15
5 0.23 0.15 0.18 0.17 1.00 0.14 0.16 0.13 0.16 0.15
6 0.12 0.15 0.14 0.17 0.14 1.00 0.15 0.15 0.20 0.14
7 0.13 0.15 0.13 0.15 0.16 0.15 1.00 0.14 0.12 0.12
8 0.16 0.17 0.16 0.17 0.13 0.15 0.14 1.00 0.13 0.17
9 0.13 0.12 0.14 0.16 0.16 0.20 0.12 0.13 1.00 0.12
10 0.16 0.15 0.17 0.15 0.15 0.14 0.12 0.17 0.12 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