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Status: Done started: 2017-Apr-12 04:49:09 UTC
Project NameGeeta
SequenceMATTTLNDSVTTTLASEPQRTYQVVVAATKEMGIGKDGKLPWNLPTDLKFFKDITLTTSDSSKKNAVVMGRKTWESIPIK YRPLSGRLNVVLTRSGGFDIANTENVVTCSSVDSALDLLAAPPYCLSIERVFVIGGGDILREALNRPSCDAIHLTEIDTS VDCDTFIPAIDTSVYQPWSSSFPVTENGLRFCFTTFVRVKSSADESSDESNGSQSLQFDGKKFLFLPKMVFDQHEEFLYL NMVEDIISNGNVKNDRTGTGTLSKFGCQMKFNLRRSFPLLTTKRVFWRGVVEELLWFISGSTNAKVLQEKGIHIWDGNAS REYLDGIGLTEREEGDLGPVYGFQWRHFGAKYTDMHADYTGQGFDQLVDVIDKIKNNPDDRRIIMSAWNPSDLKLMALPP CHMFAQFYVAEGELSCQMYQRSADMGLGVPFNIASYSLLTCMLAHVCDLVPGDFIHVLGDAHVYKTHVRPLQEQLLNLPK PFPVMKINPEKKQIDSFVASDFDLTGYDPHKKIEMKMAV
Secondary structure

CCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCC CCCCCCCCEEEECCCCCCCCCCCCCEEEECCHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHCCCCCCEEEEEEECCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHCCCCEECCCCCC HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCC CEEEEEEEEECCEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHCCCCCHHHHHHHHCCCC CCCCEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Apr-12 18:44 UTC

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

Cluster #12345678
Cluster density7.76.05.31.21.10.50.40.3
Cluster size135599418308106
Average cluster RMSD17.69.917.615.626.516.722.421.0

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 30.80 35.10 42.20 42.60 0.15 58.10 7.73
2 30.80 0.00 27.20 45.00 43.30 1.37 55.90 6.69
3 35.10 27.20 0.00 40.50 45.70 62.80 51.10 4.82
4 42.20 45.00 40.50 0.00 34.90 46.20 34.70 50.50
5 42.60 43.30 45.70 34.90 0.00 48.60 39.00 49.70
6 0.15 1.37 62.80 46.20 48.60 0.00 43.30 49.10
7 58.10 55.90 51.10 34.70 39.00 43.30 0.00 44.90
8 7.73 6.69 4.82 50.50 49.70 49.10 44.90 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 0.10 0.09 0.10 0.07 0.09 0.05 0.07
2 0.10 1.00 0.09 0.08 0.07 0.07 0.05 0.06
3 0.09 0.09 1.00 0.08 0.08 0.07 0.05 0.07
4 0.10 0.08 0.08 1.00 0.07 0.08 0.05 0.07
5 0.07 0.07 0.08 0.07 1.00 0.06 0.04 0.08
6 0.09 0.07 0.07 0.08 0.06 1.00 0.05 0.06
7 0.05 0.05 0.05 0.05 0.04 0.05 1.00 0.05
8 0.07 0.06 0.07 0.07 0.08 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