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Status: Done started: 2017-Apr-10 20:43:37 UTC
Project Namepract7
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-11 10:38 UTC

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

Cluster #12345678
Cluster density13.19.33.31.20.90.80.80.5
Cluster size1168973251912197
Average cluster RMSD8.89.622.220.121.014.922.615.1

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 25.30 31.80 40.60 35.90 54.80 53.00 0.96
2 25.30 0.00 28.60 36.60 37.00 53.30 51.70 65.20
3 31.80 28.60 0.00 31.70 39.70 53.50 51.90 65.40
4 40.60 36.60 31.70 0.00 38.50 38.80 41.80 49.30
5 35.90 37.00 39.70 38.50 0.00 45.30 35.30 54.40
6 54.80 53.30 53.50 38.80 45.30 0.00 38.60 30.30
7 53.00 51.70 51.90 41.80 35.30 38.60 0.00 42.20
8 0.96 65.20 65.40 49.30 54.40 30.30 42.20 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.

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