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Status: Done started: 2018-Mar-11 22:19:18 UTC
Project Named4_genI
SequenceMRCVGVGNRDFVEGVSGGAWVDLVLEHGGCVTTMAQGKPTLDFELIKTTAKEVALLRTYCIEASISNITTATRCPTQGEP YLKEEQDQQYICRRDVVDRGWGNGCGLFGKGGVVTCAKFSCSGKITGNLVQIENLEYTVVVTVHNGDTHAVGNDTSNHGE TATITPRSPSVEVKLPDYGELTLDCEPRSGIDFNEMILMKMKTKTWLVHKLCFLDLPLPWTAGADTSEVHWNHKERMVTF KVPHAKRQDVTVLGSQEGAMHSALAGATEVDSGDGNHMFAGHLKCKVRMEKLRIKGMSYTMCSGKFSIDKEMAETQHGTT VVKIKYEGTGAPCKVPIEIRDVNKEKVVGRIISSTPFAENTNSVTNIELEPPFGDSYIVIGVGDSALTLHWFRKG
Secondary structure

CEEEECCCCCCCCCCCCCEEEEEEEECCCEEEEECCCCCCCEEEEEECCHHHHHHHHHEEEEEEEECCCCCCCCCCCCCC CCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEECCCCCCEEEECCEEEEEEEEEECCCEEEECCCCCCCCE EEEECCCCCEEEEECCCCCEEEEEECCCCCCCCCCEEEEEECCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEE ECCCCCCCEEEEEECCCCHHHHHCCCCEEEECCCCCEEEEECEEEEEECCEEEEECEEEEEEECEEEEEEHHHHCCCCEE EEEEEECCCCCCEECCEEEECCCCEEEEEEEEEECCEEECCCCEEEEEECCCCCCEEEEEEECCCCEEEEEEECC

Simulation (CABS) temperature2.0 - 1.0
Estimated finish time2018-Mar-12 11:14 UTC

Provided templates.

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

Cluster #123456789
Cluster density74.568.858.249.842.031.024.517.315.6
Cluster size676049504031272016
Average cluster RMSD0.90.90.81.01.01.01.11.21.0

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 1.23 1.35 1.19 1.27 1.12 1.60 1.54 1.62
2 1.23 0.00 1.08 1.09 1.32 1.04 1.48 2.00 1.67
3 1.35 1.08 0.00 0.94 1.26 1.05 1.24 1.96 1.37
4 1.19 1.09 0.94 0.00 0.96 0.91 1.07 1.63 1.22
5 1.27 1.32 1.26 0.96 0.00 1.09 1.28 1.69 1.37
6 1.12 1.04 1.05 0.91 1.09 0.00 1.21 1.64 1.28
7 1.60 1.48 1.24 1.07 1.28 1.21 0.00 1.72 1.17
8 1.54 2.00 1.96 1.63 1.69 1.64 1.72 0.00 1.54
9 1.62 1.67 1.37 1.22 1.37 1.28 1.17 1.54 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 0.91 0.90 0.92 0.92 0.92 0.90 0.93 0.89
2 0.91 1.00 0.93 0.96 0.94 0.96 0.95 0.86 0.91
3 0.90 0.93 1.00 0.95 0.94 0.95 0.94 0.86 0.92
4 0.92 0.96 0.95 1.00 0.96 0.96 0.95 0.88 0.94
5 0.92 0.94 0.94 0.96 1.00 0.96 0.94 0.88 0.93
6 0.92 0.96 0.95 0.96 0.96 1.00 0.96 0.88 0.93
7 0.90 0.95 0.94 0.95 0.94 0.96 1.00 0.86 0.93
8 0.93 0.86 0.86 0.88 0.88 0.88 0.86 1.00 0.88
9 0.89 0.91 0.92 0.94 0.93 0.93 0.93 0.88 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