Protein structure prediction of the E. Coli proteome by TASSER
In this webpage, we present the result of protein structure predictions by the TASSER (Threading ASSEmbly Refinement) algorithm on 1360 ORFs in the E. Coli genome with length below 201 residues. Please refer to the following paper for details:
Y. Zhang, J. Skolnick. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc. Natl. Acad. Sci. USA 2004 101: 7594-7599. PDF
Summary of folding results:
- ID --- PDB code of the proteins
- Sequence --- Sequence files of target proteins
- Class --- Secondary structure classification according to the prediction from PSIPRED
- a --- alpha-protein
- b --- beta-protein
- ab --- alpha/beta-protein
- l --- protein with little secondary structures
- Length --- Number of residues of the target proteins
- Template --- Template files (in PDB format) by the threading program PROSPECTOR_3
- Z-score --- The highest Z-score in PROSPECTOR_3 hits
- Cover_ali --- Coverage of threading alignment for the highest Z-score template
- Models --- Top five models generated by clustering the trajectories by the SPICKER algorithm
- model[1-5].pdb: Cluster centroid
- close[1-5].pdb: Structures closest to the cluster centroid
- Confidence --- Probability of the top five clusters having an RMSD to native below 6.5 Angstrom. This confidence was obtained by the comparison of C-score with PDB benchmark results, where C-score is a combination of the Z-score of threading templates and the structure density in the Monte Carlo trajectories.
- a --- alpha-protein
- b --- beta-protein
- ab --- alpha/beta-protein
- l --- protein with little secondary structures
- model[1-5].pdb: Cluster centroid
- close[1-5].pdb: Structures closest to the cluster centroid
[Table I]
[Table II]
[Table III]
[Table IV]
[Table V]