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Status: Done started: 2015-Jul-13 09:28:24 UTC
Project NameCTF_I2
SequenceMHHHHHHYGRKKRRQRRRMEDQRDLISNHEQLPILGQRPAAPESKSSRGALYTGFSVLVALLLAGQATTAYFLYQQQGRL DKLTVTAQNLQLENLRMKLPKPAKPLNKLRVATPMLMQTMPVRGLLQAEDIWKVNKKSTSGGKNQDRKLDQIIQKGQQVK IQNISKLIRDKPHTNQEKEKLMKFLKKVSKGYRGASDGNISYLSRPSNLGPDWKVSKESKDPNNKDSRPTEIVPYRQQLA IPNISKLKNSETNEDSKLKKHSKEKSRGGNDAGSDGNFSYSRPKNK
Secondary structure

CCCCCCCCCCCHHHHCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCC CCEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCHH HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Jul-13 23:23 UTC

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

Cluster #123456789
Cluster density5.04.33.43.22.11.31.10.70.5
Cluster size615368564429241510
Average cluster RMSD12.312.320.317.521.021.922.222.220.5

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.

#123456789
1 0.00 25.30 27.90 23.60 25.90 32.50 29.10 31.70 31.60
2 25.30 0.00 28.50 22.40 24.60 26.20 29.30 28.20 32.20
3 27.90 28.50 0.00 27.60 29.70 26.70 27.60 29.10 26.80
4 23.60 22.40 27.60 0.00 21.60 28.20 31.00 27.10 27.20
5 25.90 24.60 29.70 21.60 0.00 31.30 28.20 27.30 25.80
6 32.50 26.20 26.70 28.20 31.30 0.00 32.20 28.20 27.30
7 29.10 29.30 27.60 31.00 28.20 32.20 0.00 29.90 25.50
8 31.70 28.20 29.10 27.10 27.30 28.20 29.90 0.00 28.30
9 31.60 32.20 26.80 27.20 25.80 27.30 25.50 28.30 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.

#123456789
1 1.00 0.14 0.11 0.12 0.08 0.13 0.12 0.08 0.10
2 0.14 1.00 0.09 0.14 0.13 0.14 0.14 0.07 0.10
3 0.11 0.09 1.00 0.10 0.11 0.10 0.08 0.09 0.12
4 0.12 0.14 0.10 1.00 0.09 0.12 0.12 0.07 0.09
5 0.08 0.13 0.11 0.09 1.00 0.12 0.07 0.08 0.11
6 0.13 0.14 0.10 0.12 0.12 1.00 0.12 0.07 0.11
7 0.12 0.14 0.08 0.12 0.07 0.12 1.00 0.07 0.09
8 0.08 0.07 0.09 0.07 0.08 0.07 0.07 1.00 0.08
9 0.10 0.10 0.12 0.09 0.11 0.11 0.09 0.08 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