Download models Download trajectory View trajectory
Status: Done started: 2017-Sep-12 23:31:28 UTC
Project NameHIF1a
SequenceMEGAGGANDKKKISSERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVSSHLDKASVMRLTISYLRVRKLLDAGDLDI EDDMKAQMNCFYLKALDGFVMVLTDDGDMIYISDNVNKYMGLTQFELTGHSVFDFTHPCDHEEMREMLTHRNGLVKKGKE QNTQRSFFLRMKCTLTSRGRTMNIKSATWKVLHCTGHIHVYDTNSNQPQCGYKKPPMTCLVLICEPIPHPSNIEIPLDSK TFLSRHSLDMKFSYCDERITELMGYEPEELLGRSIYEYYHALDSDHLTKTHHDMFTKGQVTTGQYRMLAKRGGYVWVETQ ATVIYNTKNSQPQCIVCVNYVVSGIIQHDLIFSLQQTECVLKPVESSDMKMTQLFTKVESEDTSSLFDKLKKEPDALTLL APAAGDTIISLDFGSNDTETDDQQLEEVPLYNDVMLPSPNEKLQNINLAMSPLPTAETPKPLRSSADPALNQEVALKLEP NPESLELSFTMPQIQDQTPSPSDGSTRQSSPEPNSPSEYCFYVDSDMVNEFKLELVEKLFAEDTEAKNPFSTQDTDLDLE MLAPYIPMDDDFQLRSFDQLSPLESSSASPESASPQSTVTVFQQTQIQEPTANATTTTATTDELKTVTKDRMEDIKILIA SPSPTHIHKETTSATSSPYRDTQSRTASPNRAGKGVIEQTEKSHPRSPNVLSVALSQRTTVPEEELNPKILALQNAQRKR KMEHDGSLFQAVGIGTLLQQPDDHAATTSLSWKRVKGCKSSEQNGMEQKTIILIPSDLACRLLGQSMDESGLPQLTSYDC EVNAPIQGSRNLLQGEELLRALDQVN
Secondary structure

CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCC HHHHHHHHHHHHHHHCCCEEEEECCCCCEEEECCCHHHCCCCCCEEECCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC CCCCCCEEEECCCCCCCCCCCCCCCCCCEEEEEECCEEEECCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCCCCCCCCCEEEECCCCEEEEEEC EEEEECCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCHHHHCC CCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE EECCCCCCCCCCCCHHHHHHHHHCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2017-Sep-13 13:26 UTC

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

Cluster #12345678
Cluster density31.610.02.01.61.41.31.10.5
Cluster size1261213425192078
Average cluster RMSD4.012.117.015.813.515.06.516.3

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 57.20 36.90 36.60 45.20 53.10 44.80 48.10
2 57.20 0.00 42.10 53.80 60.10 14.70 9.80 63.40
3 36.90 42.10 0.00 43.20 54.30 65.50 52.10 56.10
4 36.60 53.80 43.20 0.00 51.60 50.00 45.20 36.20
5 45.20 60.10 54.30 51.60 0.00 46.40 61.30 48.00
6 53.10 14.70 65.50 50.00 46.40 0.00 45.10 39.70
7 44.80 9.80 52.10 45.20 61.30 45.10 0.00 45.00
8 48.10 63.40 56.10 36.20 48.00 39.70 45.00 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 0.23 0.24 0.13 0.17 0.16 0.07 0.09
2 0.23 1.00 0.26 0.12 0.16 0.16 0.06 0.09
3 0.24 0.26 1.00 0.13 0.17 0.16 0.06 0.09
4 0.13 0.12 0.13 1.00 0.10 0.13 0.06 0.08
5 0.17 0.16 0.17 0.10 1.00 0.13 0.09 0.08
6 0.16 0.16 0.16 0.13 0.13 1.00 0.06 0.08
7 0.07 0.06 0.06 0.06 0.09 0.06 1.00 0.07
8 0.09 0.09 0.09 0.08 0.08 0.08 0.07 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