NMRtist Use Cases
Written by: Piotr Klukowski
Published: July 29, 2024, 10:03 a.m.
List of the most common NMRtist use cases:
The table below lists the input files that can be used with the NMRtist applications. These inputs play a role in different use case scenarios where the assistance of the platform in data analysis is possible.
By understanding the specific uses and formats of these input files, users can effectively leverage the capabilities of NMRtist to enhance their data analysis workflows.
| Input file | Data types | Practical application | Example source |
|---|
| Peak list | Sparky (*.list), XEASY (*.peaks) | Provides manual peak lists as input for the NMRtist application | Manual peak picking
Manually refined output of the automated peak picking |
| Chemical shift statistic | XEASY (*.stats) | Defines chemical shifts for the automated chemical shift transfer | Assignment of source protein that is used for transfer
Chemical shift predictions (e.g. UCBShift) based on AlphaFold structure |
| Chemical shift list | XEASY (*.prot) | Provides partial assignment for the automated chemical shift completion | Incomplete list of manually assign chemical shifts
Manually refined output of the automated chemical shift assignment |
| Protein structure | PDB (*.pdb) | Defines the protein fold for the automated structure-based chemical shift assignment | Protein model obtained with experimental methods
In-silico prediction (e.g. AlphaFold) |
| Distance restraints | CYANA (*.upl. *.lol)) | Defines distance restraints to be used in the protein structure calculation | Distance restraints obtained in experiments not reported in NMRtist project |
| Angle restraints | TALOS (*.aco) | Defines angle restraints to be used in the protein structure calculation | Angle restraints obtained in experiments not reported in NMRtist project |
Automated peak picking
- Create and open NMRtist project
- Upload NMR spectra to the project storage
- Run the application "ARTINA: peak picking" using the NMR spectra you would like to analyze as the input.
Automated de novo chemical shift assignment
- Create and open NMRtist project
- Upload NMR spectra to the project storage
- Run application "ARTINA: peak picking" using NMR spectra you would like to analyze as the input.
- Verify that the output of the automated peak picking does not contain any anomalies, especially those related to spectra referencing.
- Run application "ARTINA: chemical shift assignment" using NMR spectra you would like to analyze as the input.
Automated de novo structure determination of protein monomer
- Create and open NMRtist project
- Upload NMR spectra to the project storage
- Run application "ARTINA: peak picking" using NMR spectra you would like to analyze as the input.
- Verify that the output of the automated peak picking does not contain any anomalies, especially those related to spectra referencing.
- Run application "ARTINA: structure determination" using NMR spectra you would like to analyze as the input.
Automated de novo chemical shift assignment and structure determination of protein-ligand complex
- Prepare CYANA library file with definition of the ligand
- Create NMRtist project using CYANA sequence (*.seq) and ligand definition (*.lib). Open the project.
- Upload NMR spectra to the project storage
- Run application "ARTINA: peak picking" using NMR spectra you would like to analyze as the input.
- Verify that the output of the automated peak picking does not contain any anomalies, especially those related to spectra referencing.
- Run application "ARTINA: chemical shift assignment" or "ARTINA: structure determination" using NMR spectra you would like to analyze as the input.
Automated chemical shift transfer
Chemical shift transfer allows finding the unknown assignment of the target protein, given a limited set of spectra of the target protein and the known assignment of the source protein.
The chemical shifts of the source and target proteins must be similar, but not necessarily identical.
- Create and open NMRtist project
- Upload NMR spectra of target protein to the project storage
- Prepare and upload *.stat file with chemical shifts and their tolerances of the source protein. Example *.stat file is available in user manual
- Run application "ARTINA: peak picking" using NMR spectra you would like to analyze as the input.
- Verify that the output of the automated peak picking does not contain any anomalies, especially those related to spectra referencing.
- Run application "ARTINA: chemical shift assignment" using NMR spectra and *.stat file as the input. NMRtist will automatically recognize *.stat file in the input and trigger the chemical shift transfer.
Automated structure based chemical shift assignment
Structure-based chemical shift assignment assigns the chemical shifts of a protein given its NMR spectra and protein structure.
This use case is designed for NMR studies, where the fold of the protein is known. Alternatively, one can use AlphaFold prediction as the input, if experimental structure (e.g. X-ray) is not available.
An extensive evaluation of this procedure is available in our manuscript (
doi/full/10.1126/sciadv.adi9323).
- Create and open NMRtist project
- Upload NMR spectra of target protein to the project storage
- Upload *.pdb file with structure model to be used for structure based assignment
- Run application "ARTINA: peak picking" using NMR spectra you would like to analyze as the input.
- Verify that the output of the automated peak picking does not contain any anomalies, especially those related to spectra referencing.
- Run application "ARTINA: chemical shift assignment" using NMR spectra and *.pdb file as the input. NMRtist will automatically recognize *.pdb file in the input and trigger the structure-based assignment.
Automated completion of incomplete manual assignment
This use case is applicable when a partial assignment (e.g., backbone) is available from previous studies, and the objective is to find the complete assignment given newly recorded spectra (i.e., backbone and side-chain).
- Create and open NMRtist project
- Upload NMR spectra of target protein to the project storage
- Prepare and upload *.prot file with known chemical shifts. Example is available in user manual
- Run application "ARTINA: peak picking" using NMR spectra you would like to analyze as the input.
- Verify that the output of the automated peak picking does not contain any anomalies, especially those related to spectra referencing.
- Run application "ARTINA: chemical shift assignment" using NMR spectra and *.prot file as the input. NMRtist will automatically recognize *.prot file in the input and trigger the chemical shift completion.
Manual refinement of NMRtist results
The results obtained through NMRtist automated data analysis can be refined manually using the "human-in-the-loop" procedure.
- Analyze results of the NMRtist job and identify the bottleneck. For example, if you find atoms with weak assignments in the protein backbone, the problem might be linked to insufficient number of peaks identified in the backbone spectra. If you identify that number of NOEs is insufficient, the problem might be linked to insufficient number of cross-peaks detected in the NOESY spectra.
- Manually refine the identified bottleneck. For example, if the problem is linked to an insufficient number of cross-peaks detected in the C13NOESY spectrum, download the C13NOESY peak list from the NMRtist results, open it in dedicated NMR software (e.g., Sparky, CCPN), and refine by removing wrongly identified peaks (false positive predictions) and adding missing peaks (false negative predictions).
- Upload the refined file to your NMRtist project
- Use the refined file as input for the application call. Note: If you provide a refined peak list, use it instead of the corresponding NMR spectrum.
Frequently Asked Questions
How do I handle sequences with custom residues?
To work with custom residues, you can define them in a CYANA library file and include them in your sequence file. These custom library and sequence files can then be used to create a new project. Once the project is created, handling custom sequences is the same as working with standard amino acid sequences. During runtime, NMRtist applications automatically recognize and handle custom residues.
How do I handle disulfide bridges?
For cysteines involved in forming disulfide bridges, mark them as CYSS in the protein sequence. If you have information about specific pairs of cysteines that form bridges, this can be provided in a *.upl file.