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Status: Done started: 2014-Feb-04 13:56:24 UTC
Project NameLDH1
SequenceMASTIKEVFAEIAAPVENSHGKVTVVGVGQVGMACAYSILQQNLANELCLVDVVADKLKGEMMDLQHGLAFTRHCTVKAD TDYSITAGSKLCVVTAGARQREGETRLSLVQRNVEIFKGIIPQLVKYSPDTCILVVSNPVDVLTYVTWKLSGLPRERVFG SGTNLDSARFRFLLSEKLNIAPSSCHGWIIGEHGDSSVAVWSGVNVAGVTLHEIKPDIGEKTDNEHWEAEIHKKVVDSAY EIIKLKGYTSWAIGLSVAKIAQGIFSNSRNVFALSTNVKGFHGINDDVYLSLPVVLGSAGLTHVVKQQLTEAEVQKLHNS AKALLEVQNGIVM
Secondary structure

CCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCHHCCCCCCCCCCCCCEECC CCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHCCCCCCCEEC CCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH HHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCEEEECCEEECCCCCCEEECCCCCHHHHHHHHHH HHHHHHHHHCCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2014-Feb-05 02:51 UTC

Provided templates.

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

Cluster #123456789
Cluster density161.1148.7148.082.964.448.044.232.110.1
Cluster size63617747342925186
Average cluster RMSD0.40.40.50.60.50.60.60.60.6

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 1.59 1.64 2.48 1.65 1.47 2.48 1.52 1.68
2 1.59 0.00 2.27 2.47 1.46 1.88 2.62 1.65 2.34
3 1.64 2.27 0.00 2.96 1.95 1.95 2.71 2.06 1.27
4 2.48 2.47 2.96 0.00 2.43 2.50 2.90 2.57 3.05
5 1.65 1.46 1.95 2.43 0.00 1.98 2.70 1.58 2.00
6 1.47 1.88 1.95 2.50 1.98 0.00 2.41 1.79 2.12
7 2.48 2.62 2.71 2.90 2.70 2.41 0.00 1.99 2.76
8 1.52 1.65 2.06 2.57 1.58 1.79 1.99 0.00 2.07
9 1.68 2.34 1.27 3.05 2.00 2.12 2.76 2.07 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 0.90 0.90 0.89 0.91 0.86 0.82 0.91 0.87
2 0.90 1.00 0.90 0.87 0.88 0.82 0.78 0.86 0.84
3 0.90 0.90 1.00 0.90 0.93 0.87 0.85 0.89 0.89
4 0.89 0.87 0.90 1.00 0.91 0.86 0.81 0.89 0.87
5 0.91 0.88 0.93 0.91 1.00 0.86 0.85 0.90 0.89
6 0.86 0.82 0.87 0.86 0.86 1.00 0.83 0.85 0.79
7 0.82 0.78 0.85 0.81 0.85 0.83 1.00 0.83 0.82
8 0.91 0.86 0.89 0.89 0.90 0.85 0.83 1.00 0.85
9 0.87 0.84 0.89 0.87 0.89 0.79 0.82 0.85 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.


 

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