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Status: Done started: 2013-Nov-23 13:17:20 UTC
Project Namerod-1165-1770
SequenceRQCQMDDCGILMKASFGTHKDPYEEWSYSDFFSEDGIVLESQMVLPVIYELISSLVPLAESKRYPLESTSLPYCSLNEGD GLVLPVINSISALLQNLQESSQWELALRFVVGSFGTCLQHSVSNFMNATLSEKLFGETTLVKSRHVVMELKEKAVIFIRE NATTLLHKVFNCRLVDLDLALGYCTLLPQKDVFENLWKLIDKAWQNYDKILAISLVGSELASLYQEIEMGLKFRELSTDA QWGIRLGKLGISFQPVFRQHFLTKKDLIKALVENIDMDTSLILEYCSTFQLDCDAVLQLFIETLLHNTNAGQGQGDASMD SAKRRHPKLLAKALEMVPLLTSTKDLVISLSGILHKLDPYDYEMIEVVLKVIERADEKITNININQALSILKHLKSYRRI SPPVDLEYQYMLEHVITLPSAAQTRLPFHLIFFGTAQNFWKILSTELSEESFPTLLLISKLMKFSLDTLYVSTAKHVFEK KLKPKLLKLTQAKSSTLINKEITKITQTIESCLLSIVNPEWAVAIAISLAQDIPEGSFKISALKFCLYLAERWLQNIPSQ DEKREKAEALLKKLHIQYRRSGTEAVLIAHKLNTEEYLRVIGKPA
Secondary structure

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC CCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHC HHHHHHHCCCCCCCHHHHHCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCC CCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCC CCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH HHCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2013-Nov-24 02:12 UTC

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

Cluster #1234567
Cluster density20.48.25.92.11.91.40.9
Cluster size126766538172414
Average cluster RMSD6.29.211.118.28.816.815.9

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.

#1234567
1 0.00 30.00 45.90 30.80 49.10 41.80 61.40
2 30.00 0.00 47.20 33.00 42.90 38.30 56.20
3 45.90 47.20 0.00 41.20 40.40 40.60 43.60
4 30.80 33.00 41.20 0.00 47.30 40.10 57.00
5 49.10 42.90 40.40 47.30 0.00 38.90 37.00
6 41.80 38.30 40.60 40.10 38.90 0.00 45.20
7 61.40 56.20 43.60 57.00 37.00 45.20 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.

#1234567
1 1.00 0.07 0.07 0.07 0.06 0.06 0.05
2 0.07 1.00 0.07 0.07 0.07 0.06 0.05
3 0.07 0.07 1.00 0.07 0.06 0.07 0.06
4 0.07 0.07 0.07 1.00 0.07 0.05 0.05
5 0.06 0.07 0.06 0.07 1.00 0.05 0.06
6 0.06 0.06 0.07 0.05 0.05 1.00 0.05
7 0.05 0.05 0.06 0.05 0.06 0.05 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