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Status: Done started: 2018-Mar-03 13:36:34 UTC
Project NameHKU1
SequenceIKPVLFVDQYGCDYSGKLADCLQAYGHYSLQDMRQKQSVWLANCDFDIVVAWHVVRDSRFVMRLQTIATICGIKYVAQPT EDVVDGDVVIREPVHLLSADAIVLKLPSLMKVMTHMDDFSIKSIYNVDLCDCGFVMQYGYVDCFNDNCDFYGWVSGNMMD GFSCPLCCTVYDSSEVKAQSSGVIPENPVLFTNSTDTVNPDSFNLYGYSVTPFGSCIYWSPRPGLWIPIIKSSVKSYDDL VYSGVVGCKSIVKETALITHALYLDYVQCKCGNLEQNHILGVNNSWCRQLLLNRGDYNMLLKNIDLFVKRRADFACKFAV CGDGFVPFLLDGLIPRSYYLIQSGIFFTSLMSQFSQEVSDMCLKMCILFMDRVSVATFYIEHYVNRLVTQFKLLGTTLVN KMVNWFNTMLDASAPATGWLLYQLLNGFFVVSQANLNFVALIPDYAKILVNKFYTFFKLLLECVTVDVLKDMPVLKTING LVCIVGNKFYNVSTGLIPGFVLPCNAQEQQIYFFEGVAESVIVEDDVIENVKSSLSSYEYCQPPKSVEKICIIDNMYMGK CGDKFFPIVMNDKNICLLDHAWRFPCA
Secondary structure

CCCEEEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHCHHHCCCCCCCEEEEEEEEECCCCCCCCCEEEEEEEEEEECCCC CCCCCCCEEEECCCEEECCCHHHHCCHHHHHHHHCCCCCEEEEECCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCEEEECCCCCCCCEEEECCCCCCCCCCEEECCEEEEECCCEEEECCCCCCCCCEEECCCCCCCCE EEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCCCCHHHHHHHHHCCCCCHHHHCCCHHHHHHCCCCCCCEEEE ECCCCCHHHCCCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHCCCHHHHHHHHHHCCEEEEEECEEEEEECCHHHHHHHHHHHHHHHHHHHHEEEEEEECCCCEEEECCC EEEEECCEEEEEECCCCCCEEECCCCCCCEEEEEEEEEEEEEEECCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEC CCCEEEEEEECCCEEECCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Mar-04 02:31 UTC

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

Cluster #12345678
Cluster density22.111.51.81.41.11.11.10.5
Cluster size14711222182219155
Average cluster RMSD6.79.712.013.219.618.013.19.4

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.

#12345678
1 0.00 28.80 46.90 33.30 35.10 47.20 3.10 3.90
2 28.80 0.00 47.40 31.20 31.70 48.10 4.36 5.14
3 46.90 47.40 0.00 44.40 32.70 42.70 37.60 46.70
4 33.30 31.20 44.40 0.00 29.70 37.40 61.70 63.10
5 35.10 31.70 32.70 29.70 0.00 35.60 51.40 52.90
6 47.20 48.10 42.70 37.40 35.60 0.00 49.50 49.60
7 3.10 4.36 37.60 61.70 51.40 49.50 0.00 38.90
8 3.90 5.14 46.70 63.10 52.90 49.60 38.90 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.

#12345678
1 1.00 0.11 0.08 0.10 0.11 0.08 0.06 0.06
2 0.11 1.00 0.09 0.11 0.11 0.09 0.06 0.06
3 0.08 0.09 1.00 0.09 0.10 0.08 0.07 0.06
4 0.10 0.11 0.09 1.00 0.11 0.07 0.05 0.05
5 0.11 0.11 0.10 0.11 1.00 0.08 0.05 0.07
6 0.08 0.09 0.08 0.07 0.08 1.00 0.05 0.05
7 0.06 0.06 0.07 0.05 0.05 0.05 1.00 0.05
8 0.06 0.06 0.06 0.05 0.07 0.05 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