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Status: Done started: 2013-Nov-30 12:16:11 UTC
Project NameChloe_test
SequenceMATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDKHEGALETLLRYYDQICSIEP KFPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYEKSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAF LHIKETVLSALSREPTVDISPDTVGTLSLIMLAQAQEVFFLKATRDKMKDAIIAKLANQAADYFGDAFKQCQYKDTLPKE VFPVLAAKHCIMQANAEYHQSILAKQQKKFGEEIARLQHAAELIKTVASRYDEYVNVKDFSDKINRALAAAKKDNDFIYH DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAAYNQRKADLVNRSIAQMREATTLANGVLASLN LPAAIEDVSGDTVPQSILTKSRSVIEQGGIQTVDQLIKELPELLQRNREILDESLRLLDEEEATDNDLRAKFKERWQRTP SNELYKPLRAEGTNFRTVLDKAVQADGQVKECYQSHRDTIVLLCKPEPELNAAIPSANPAKTMQGSEVVNVLKSLLSNLD EVKKEREGLENDLKSVNFDMTSKFLTALAQDGVINEEALSVTELDRVYGGLTTKVQESLKKQEGLLKNIQVSHQEFSKMK QSNNEANLREEVLKNLATAYDNFVELVANLKEGTKFYNELTEILVRFQNKCSDIVFARKTERDELLKDLQQSIAREPSAP SIPTPAYQSSPAGGHAPTPPTPAPRTMPPTKPQPPARPPPPVLPANRAPSATAPSPVGAGTAAPAPSQTPGSAPPPQAQG PPYPTYPGYPGYCQMPMPMGYNPYAYGQYNMPYPPVYHQSPGQAPYPGPQQPSYPFPQPPQQSYYPQQ
Secondary structure

CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC CCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2013-Dec-01 01:11 UTC

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

Cluster #123456789
Cluster density47.618.69.93.02.22.01.41.41.2
Cluster size1148940172926151416
Average cluster RMSD2.44.84.15.713.313.010.510.213.0

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 43.70 38.30 53.20 44.10 54.40 46.80 61.20 42.30
2 43.70 0.00 39.10 58.60 36.00 46.20 34.20 58.20 50.60
3 38.30 39.10 0.00 55.10 47.50 47.40 45.00 54.70 51.90
4 53.20 58.60 55.10 0.00 47.10 49.50 56.50 48.80 48.10
5 44.10 36.00 47.50 47.10 0.00 52.90 31.10 59.70 46.80
6 54.40 46.20 47.40 49.50 52.90 0.00 49.50 33.70 0.83
7 46.80 34.20 45.00 56.50 31.10 49.50 0.00 53.80 53.40
8 61.20 58.20 54.70 48.80 59.70 33.70 53.80 0.00 63.50
9 42.30 50.60 51.90 48.10 46.80 0.83 53.40 63.50 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 0.12 0.07 0.05 0.06 0.06 0.06 0.08 0.07
2 0.12 1.00 0.06 0.05 0.07 0.07 0.07 0.06 0.07
3 0.07 0.06 1.00 0.06 0.06 0.07 0.07 0.07 0.06
4 0.05 0.05 0.06 1.00 0.06 0.05 0.06 0.06 0.05
5 0.06 0.07 0.06 0.06 1.00 0.06 0.06 0.06 0.07
6 0.06 0.07 0.07 0.05 0.06 1.00 0.06 0.06 0.07
7 0.06 0.07 0.07 0.06 0.06 0.06 1.00 0.06 0.06
8 0.08 0.06 0.07 0.06 0.06 0.06 0.06 1.00 0.06
9 0.07 0.07 0.06 0.05 0.07 0.07 0.06 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