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Status: Done started: 2017-Jun-20 09:50:43 UTC
Project Namepp_p4h3
SequenceMPCPICVLSCAGMTLSLYNMKSSKNKGRKWNPFTYKLSLPQVLLWCTICLLAGYAASNFFPQKIEEEAIYQPYRKSAQQE GEFPFGEFSEKVVLDHGSTGDNFIADIPFQVLSWKPRALLYPRFASKEQCEAIMKLARTRLAPSALALRKGESEDSTKDI RTSSGTFLRADEDTTRSLEQVEEKMAKATMIPRENGEAFNVLKYNVGQKYDCHYDVFDPAEYGPQPSQRMASFLLYLSDV EEGGETMFPFENFQNMNIGFDYKKCIGMKVKPRQGDALLFYSMHPNGTFDKSALHGSCPVIKGEKWVATKWIRNTDKF
Secondary structure

CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCC CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Jun-20 23:45 UTC

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

Cluster #123456789
Cluster density15.25.83.22.41.61.11.00.60.6
Cluster size1036955363513201514
Average cluster RMSD6.812.017.214.921.511.920.823.824.9

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 12.90 19.20 25.80 25.50 28.10 29.30 27.40 32.60
2 12.90 0.00 18.50 27.30 24.50 27.70 28.40 27.80 32.80
3 19.20 18.50 0.00 26.00 24.70 30.30 25.50 26.70 29.70
4 25.80 27.30 26.00 0.00 27.00 28.00 26.30 29.70 30.20
5 25.50 24.50 24.70 27.00 0.00 34.00 23.90 23.70 22.90
6 28.10 27.70 30.30 28.00 34.00 0.00 36.40 34.50 32.80
7 29.30 28.40 25.50 26.30 23.90 36.40 0.00 24.90 27.30
8 27.40 27.80 26.70 29.70 23.70 34.50 24.90 0.00 26.90
9 32.60 32.80 29.70 30.20 22.90 32.80 27.30 26.90 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 0.23 0.16 0.09 0.08 0.09 0.07 0.07 0.06
2 0.23 1.00 0.14 0.09 0.08 0.07 0.08 0.08 0.07
3 0.16 0.14 1.00 0.09 0.07 0.07 0.07 0.08 0.06
4 0.09 0.09 0.09 1.00 0.07 0.07 0.07 0.07 0.07
5 0.08 0.08 0.07 0.07 1.00 0.07 0.07 0.10 0.07
6 0.09 0.07 0.07 0.07 0.07 1.00 0.07 0.08 0.06
7 0.07 0.08 0.07 0.07 0.07 0.07 1.00 0.08 0.06
8 0.07 0.08 0.08 0.07 0.10 0.08 0.08 1.00 0.06
9 0.06 0.07 0.06 0.07 0.07 0.06 0.06 0.06 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