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Status: Done started: 2018-Mar-06 11:08:05 UTC
Project Namemmb
SequenceMATTTLNDSVTTTLASEPQRTYQVVVAATKEMGIGKDGKLPWNLPTDLKFFKDITLTTSDSSKKNAVVMGRKTWESIPIK YRPLSGRLNVVLTRSGGFDIANTENVVTCSSVDSALDLLAAPPYCLSIERVFVIGGGDILREALNRPSCDAIHLTEIDTS VDCDTFIPAIDTSVYQPWSSSFPVTENGLRFCFTTFVRVKSSADESSDESNGSQSLQFDGKKFLFLPKMVFDQHEEFLYL NMVEDIISNGNVKNDRTGTGTLSKFGCQMKFNLRRSFPLLTTKRVFWRGVVEELLWFISGSTNAKVLQEKGIHIWDGNAS REYLDGIGLTEREEGDLGPVYGFQWRHFGAKYTDMHADYTGQGFDQLVDVIDKIKNNPDDRRIIMSAWNPSDLKLMALPP CHMFAQFYVAEGELSCQMYQRSADMGLGVPFNIASYSLLTCMLAHVCDLVPGDFIHVLGDAHVYKTHVRPLQEQLLNLPK PFPVMKINPEKKQIDSFVASDFDLTGYDPHKKIEMKMAV
Secondary structure

CCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCC CCCCCCCCEEEECCCCCCCCCCCCCEEEECCHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHCCCCCCEEEEEEECCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHCCCCEECCCCCC HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCC CEEEEEEEEECCEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHCCCCCHHHHHHHHCCCC CCCCEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2018-Mar-07 00:03 UTC

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

Cluster #12345678
Cluster density26.38.02.41.11.00.50.50.5
Cluster size12310655222381310
Average cluster RMSD4.713.222.520.322.716.126.521.0

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.

#12345678
1 0.00 34.10 38.20 45.10 35.90 56.30 47.80 6.07
2 34.10 0.00 31.50 40.40 36.70 55.10 40.60 3.30
3 38.20 31.50 0.00 33.60 40.00 49.70 40.30 61.20
4 45.10 40.40 33.60 0.00 43.30 34.50 41.40 49.70
5 35.90 36.70 40.00 43.30 0.00 54.90 44.90 3.78
6 56.30 55.10 49.70 34.50 54.90 0.00 39.30 43.40
7 47.80 40.60 40.30 41.40 44.90 39.30 0.00 45.90
8 6.07 3.30 61.20 49.70 3.78 43.40 45.90 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 0.08 0.06 0.08 0.11 0.07 0.10 0.08
2 0.08 1.00 0.09 0.09 0.09 0.07 0.07 0.08
3 0.06 0.09 1.00 0.07 0.07 0.06 0.08 0.07
4 0.08 0.09 0.07 1.00 0.09 0.07 0.07 0.07
5 0.11 0.09 0.07 0.09 1.00 0.08 0.09 0.08
6 0.07 0.07 0.06 0.07 0.08 1.00 0.07 0.07
7 0.10 0.07 0.08 0.07 0.09 0.07 1.00 0.08
8 0.08 0.08 0.07 0.07 0.08 0.07 0.08 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