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PREDITOR protocol.
Figure 1.  

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The input to the program consists of a file of assigned chemical shifts (BMRB or SHIFTY format) and the output is a set of predicted torsion angles (φ, ψ, χ, ω) and associated error limits or confidence values.  Minimally the sequential assignment input should be >80% complete with at least one set of 1Hα and/or one set of 13C shifts being available.  From the assignment table, PREDITOR determines the φ, ψ, χ,1 and ω torsion angles directly from the chemical shift data using database comparisons and various heuristic rules (see below).  After this initial calculation has been performed the program runs the same set of chemical shifts through the Random Coil Index (RCI) protocol to determine the location of the flexible regions of the query protein.  Briefly, the RCI method is technique that uses an inverse weighted sum of secondary chemical shifts to quantify protein backbone flexibility (RMSF, order parameters and torsion angle variance).  The RCI step allows probable torsion angle errors to be assigned to essentially all predicted torsion angles.  Once the shift-derived torsion angles are generated the PREDITOR program uses BLAST to check if the query protein has a protein homologue in the Protein Databank (PDB).  If a homologue is found it is downloaded and checked for the level of sequence identity and evaluated for secondary structure content.  If a homologue is found with sufficient sequence identity (>50%), the torsion angles are calculated using VADAR and mapped to the aligned portions between the query sequence and PDB homologue.  If a homologue is not found, the secondary structure content of the query protein is determined using the Chemical Shift Index.  In both cases, the secondary structure content is used in combination with the RCI values to determine the expected torsion angle errors for both the shift-derived and PDB-derived torsion angles.  In the final stages of the program the chemical shift-derived torsion angles and the PDB-derived torsion angles (if they exist) are compared and merged.  For instance, if the PDB-derived torsion angles only covered the N-terminal region of the query protein, then the shift-derived torsion angles would be used to fill in the remaining C-terminal values.  Similarly, if there were sequence gaps in the query-to-PDB alignment, the shift-derived torsion angles would be used to fill in these gaps.  Likewise, if there are significant differences (>60o) between the PDB-derived and shift-derived torsion angles, the PDB-derived angles are always over-ridden by the shift-derived data. 


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