Download models Download trajectory View trajectory
Status: Done started: 2020-Jan-01 17:37:20 UTC
Project NameCABSfold_B-actin_Y133N-NEW
SequenceMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWD DMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMNVAIQAVLSLYASGRTTGIVMDSGDGVT HTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITAL APSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF
Secondary structure

CCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCC HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCE EEEECCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHEEEECHHHHHHHHHCCCCCCCCC CCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCEEEECCCCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHC CCCCEEEEEECCCCCEEEEEECCHHHHCHHHHHHHHHCCCCCCCCCCCEEECCCC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2020-Jan-02 06:32 UTC

Provided templates.

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

Cluster #123456789
Cluster density138.5135.3114.5111.297.191.786.644.129.4
Cluster size62544053454435198
Average cluster RMSD0.40.40.30.50.50.50.40.40.3

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 0.82 1.04 0.70 0.70 0.81 0.79 0.70 0.78
2 0.82 0.00 1.09 0.71 0.64 0.90 0.75 0.79 0.90
3 1.04 1.09 0.00 0.98 1.10 1.11 0.93 1.11 1.07
4 0.70 0.71 0.98 0.00 0.60 0.78 0.70 0.70 0.70
5 0.70 0.64 1.10 0.60 0.00 0.81 0.75 0.71 0.79
6 0.81 0.90 1.11 0.78 0.81 0.00 0.89 0.76 0.84
7 0.79 0.75 0.93 0.70 0.75 0.89 0.00 0.80 0.86
8 0.70 0.79 1.11 0.70 0.71 0.76 0.80 0.00 0.88
9 0.78 0.90 1.07 0.70 0.79 0.84 0.86 0.88 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 0.97 0.92 0.98 0.98 0.95 0.95 0.98 0.96
2 0.97 1.00 0.93 0.98 0.98 0.96 0.97 0.97 0.96
3 0.92 0.93 1.00 0.94 0.92 0.91 0.95 0.91 0.91
4 0.98 0.98 0.94 1.00 0.99 0.98 0.97 0.99 0.98
5 0.98 0.98 0.92 0.99 1.00 0.98 0.97 0.98 0.97
6 0.95 0.96 0.91 0.98 0.98 1.00 0.95 0.96 0.96
7 0.95 0.97 0.95 0.97 0.97 0.95 1.00 0.96 0.95
8 0.98 0.97 0.91 0.99 0.98 0.96 0.96 1.00 0.95
9 0.96 0.96 0.91 0.98 0.97 0.96 0.95 0.95 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