Edit detail for EvaluatingTheResultsOfAutomatedStructureCalculation revision 15 of 15

Evaluating results of automated structure calculation

This page gives some tips on evaluating the results of automated structure calculation.

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UNIO

Unio includes the package AtnosCandid for automatic structure calculation. AtnosCandid automatically picks peaks in NOESY spectra, assigns them to resonances provided in the chemical shift list(s), converts them to constraints, and calculates structures using an external program (e.g. CYANA). The process is iterative: the structures generated in intermediate cycles are used to reduce the ambiguity in the assignment of peaks in later rounds resulting in the identification of additional constraints.

Covalent check: The first stage of AtnosCandid analysis is the covalent check which compares the chemical shifts in the prot file to the NOESY to see if there is agreement. This take 20m to an hr depending on the computing infrastructure. Only after this stage is completed does UNIO give information on whether the input is ok and everything is set up correctly.

To do the covalent check UNIO uses the sequence and the chemical shifts along with knowledge about covalent geometry (hence the name) to calculate a predicted set of crosspeaks in the NOESYs, the covalent peaklist. These peaks should be present independent of the structure due to short interproton distances in the amino acid chain.

Once this is completed, the user should check how well the predicted peaks match the NOESY. Missing peaks (especially a tower of them) can indicate misalignment with the actual position in the NOESY.

Here is a dedicated page on how to evaluate the Covalent peaklist: EvaluatingTheCovalentPeakList

You can also use LUA scripts like

• "ReadCyanaPeakList.lua:AllCaluaScripts reads CYANA-generated peaklists into project. Is able to handle peaks with ambiguous (multiple) assignments.
• "ShowNoesInMolmol.lua":AllCaluaScripts creates molmol macro displaying a strip-anchors atom and all candidates atoms corresponding to an NOE in the strip.
• "UplsToSpinLinks.lua":AllCaluaScripts imports the UPLs? from a structure calculation and converts them into SpinLinks visible for a selected NOESY in a CARA project.
• "ProposeAndShow.lua":AllCaluaScripts Displays contours for proposed SpinLinks in the transposed positions in different NOESY spectra
• "ImportLinksFromPeakList.lua":AllCaluaScripts Creates Spinlinks in a Project from a NOESY Peaklist