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Status: Done started: 2015-Sep-26 16:59:31 UTC
Project NameHP1
SequenceSTGDVFWRGFNRTFLENKPINLDHVCSSDFSVEECGSIAALICQSLLPCGKITCRACAAKNLNMDEDTFKEFQTQRAREI SAVIISEHPNFACVSQFIDRYFSHQRVLNPNVNAYREILKIVGGFTQSPYTHIQELNEILVLGGRATPEQLGSASAHLLE ITRFVRNRTDNIKKGSLALFRNKISAKAHVNTALMCDNQLDRNGNLIWGERGYHAKRFFSNYFDIITPGGGYKQYIERRV PNGIRKLAIGNLIVTTNLEALREQLEGESIEKKAVTKACVSMSDNNYKYPCCCVTLDDGTPLYSTFIMPTKNHLVIGNSG DPKFLDLPADISTQMYIAKSGYCYINIFLAMLVNVDESDAKDFTKKVRDIIVPDLGEWPTLIDVATSCSLLSAFYPATSA AELPRILVDHDLKTMHVIDSYGSLNTGYHVLKANTIRQLIQFASNSLDSEMKHYRVG
Secondary structure

CCHHHHCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH HHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH HHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEECCCCCCHHHHCCCCCCCCCCCCCCCCCCEECCC CCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCC CCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCC CCCCCEEEECCCCEEEEEECCCCCCCCHHHHCCCHHHHHHHHHCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Sep-27 06:54 UTC

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

Cluster #123456789
Cluster density14.14.93.42.71.11.00.90.80.5
Cluster size897966521815191210
Average cluster RMSD6.316.319.619.015.915.120.515.418.7

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.

#123456789
1 0.00 24.90 29.60 28.20 41.10 37.10 33.10 33.20 48.10
2 24.90 0.00 30.30 35.70 39.30 35.90 35.70 32.40 47.80
3 29.60 30.30 0.00 26.90 34.50 33.60 35.70 33.90 47.80
4 28.20 35.70 26.90 0.00 40.10 37.80 34.60 37.90 48.80
5 41.10 39.30 34.50 40.10 0.00 33.70 40.60 38.70 37.30
6 37.10 35.90 33.60 37.80 33.70 0.00 31.80 35.60 43.30
7 33.10 35.70 35.70 34.60 40.60 31.80 0.00 39.20 44.20
8 33.20 32.40 33.90 37.90 38.70 35.60 39.20 0.00 39.80
9 48.10 47.80 47.80 48.80 37.30 43.30 44.20 39.80 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 0.06 0.07 0.06 0.05 0.06 0.05 0.04 0.05
2 0.06 1.00 0.05 0.06 0.05 0.06 0.06 0.05 0.05
3 0.07 0.05 1.00 0.07 0.05 0.06 0.05 0.05 0.05
4 0.06 0.06 0.07 1.00 0.05 0.06 0.06 0.05 0.04
5 0.05 0.05 0.05 0.05 1.00 0.04 0.06 0.04 0.04
6 0.06 0.06 0.06 0.06 0.04 1.00 0.05 0.04 0.05
7 0.05 0.06 0.05 0.06 0.06 0.05 1.00 0.04 0.05
8 0.04 0.05 0.05 0.05 0.04 0.04 0.04 1.00 0.04
9 0.05 0.05 0.05 0.04 0.04 0.05 0.05 0.04 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