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Status: Done started: 2015-Dec-14 08:40:36 UTC
Project Namepabp1+3A
SequenceMAAAAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGLESEELEPEELLLEPEPEPEPEEEPPRP RAPPGAPGPGPGSGAPGSQEEEEEPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAG PVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLF RGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATSWYSPY
Secondary structure

CHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC CCCCCHHHHHHCCCCCEEEECCCCCCCHHHHHHHHCCCCCCCEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCC CCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2015-Dec-14 21:35 UTC

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

Cluster #123456789
Cluster density18.63.42.92.81.91.71.71.21.0
Cluster size605748314542262724
Average cluster RMSD3.216.616.311.123.924.415.622.724.1

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 29.50 28.80 28.00 32.80 28.50 27.40 27.50 29.40
2 29.50 0.00 32.70 33.90 28.50 32.20 30.30 36.80 33.80
3 28.80 32.70 0.00 29.70 33.70 29.20 29.20 34.40 31.60
4 28.00 33.90 29.70 0.00 32.80 35.90 27.80 31.80 31.00
5 32.80 28.50 33.70 32.80 0.00 34.00 29.40 35.60 36.30
6 28.50 32.20 29.20 35.90 34.00 0.00 27.90 36.40 32.20
7 27.40 30.30 29.20 27.80 29.40 27.90 0.00 31.90 29.00
8 27.50 36.80 34.40 31.80 35.60 36.40 31.90 0.00 35.00
9 29.40 33.80 31.60 31.00 36.30 32.20 29.00 35.00 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 0.11 0.09 0.10 0.10 0.09 0.11 0.10 0.11
2 0.11 1.00 0.09 0.10 0.11 0.10 0.10 0.10 0.10
3 0.09 0.09 1.00 0.10 0.09 0.09 0.11 0.09 0.08
4 0.10 0.10 0.10 1.00 0.11 0.10 0.11 0.10 0.09
5 0.10 0.11 0.09 0.11 1.00 0.10 0.14 0.10 0.11
6 0.09 0.10 0.09 0.10 0.10 1.00 0.10 0.10 0.09
7 0.11 0.10 0.11 0.11 0.14 0.10 1.00 0.09 0.10
8 0.10 0.10 0.09 0.10 0.10 0.10 0.09 1.00 0.11
9 0.11 0.10 0.08 0.09 0.11 0.09 0.10 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