Common Usage

This video demostrates how to import NMR data from Bruker into Poky and edit the imported data.

In addition to the individual conversion, users can convert multiple processed NMR data into spectrum files and import them by one-effort.

Poky also provides a program for editing spectrum files.

This video demonstrates how to prepare a protein backbone assignment using Poky.

• Contour setting

• Synchronization of views

• Manual peak picking

• Spectral alignment

• Sequence loading

• Creating a project file

Further information of manual backbone assignment:

• Manual Backbone Assignments (2020) – National Magnetic Resonance Facility at Madison – UW–Madison (wisc.edu)

This video demonstrates how to calculate the 3D structure of the protein with Poky Structure.

Poky Structure Builder provides handy methods to import data:

• Import data from opened spectra by a few clicks.

• Drag-and-drop data from the work folder.

Recommended guideline for 3D structure calculation:

• Initial: run several times of AUDANA/AUDASA automation to get an adequate amount of constraints.

• Refinement: run several times of Constraints-only X until you get a reasonable result.

• Final: run both implicit and explicit water refinements and choose better result as the final.

This video demonstrates how to use Poky Structure Analyzer to investigate calculated 3D structures of a protein.

GUIs for the restraint refinement:

• Angle constraint validator

• Distance constraint validator (with H-bond manager)

• Contact manager

Visual validators:

• NOE bar chart

• Ramachandran plot

• Residue analysis (RMSDs, secondary structures, angle deviations, random coil index, etc.)

• Contact map

• RDC analysis