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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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mrtailor: a tool for PDB-file preparation for the generation of external restraints
1Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
Abstract:
Model building starting from, for example, a molecular-replacement solution with low sequence similarity introduces model bias, which can be difficult to detect, especially at low resolution. The program mrtailor removes low-similarity regions from a template PDB file according to sequence similarity between the target sequence and the template sequence and maps the target sequence onto the PDB file. The modified PDB file can be used to generate external restraints for low-resolution refinement with reduced model bias and can be used as a starting point for model building and refinement. The program can call ProSMART [Nicholls et al. (2012), Acta Cryst. D68, 404-417] directly in order to create external restraints suitable for REFMAC5 [Murshudov et al. (2011), Acta Cryst. D67, 355-367]. Both a command-line version and a GUI exist.
Insights
The program mrtailor reduces model bias in low-resolution crystallographic refinement by removing low-similarity regions from template PDB files. This improves model building and refinement accuracy for structural biology.
Area of Science:
- Structural Biology
- X-ray Crystallography
- Computational Biology
Background:
- Model bias is a significant challenge in low-resolution crystallographic refinement, particularly when starting from molecular replacement solutions with low sequence similarity.
- Detecting and mitigating this model bias is crucial for accurate protein structure determination.
Purpose of the Study:
- To introduce a computational tool, mrtailor, designed to reduce model bias in crystallographic model building and refinement.
- To provide a method for generating improved starting models for low-resolution structures.
Main Methods:
- The mrtailor program identifies and removes regions of low sequence similarity between a target sequence and a template PDB file.
- It then maps the target sequence onto the modified PDB file, creating a more accurate template.
- mrtailor can directly utilize ProSMART to generate external restraints compatible with REFMAC5 refinement.
Main Results:
- The modified PDB files generated by mrtailor serve as improved starting points for model building and refinement.
- Utilizing these files leads to reduced model bias, especially at low resolutions.
- The program facilitates the generation of external restraints for enhanced refinement processes.
Conclusions:
- mrtailor effectively addresses the issue of model bias in crystallographic structure determination.
- The tool enhances the accuracy of low-resolution refinements and aids in de novo model building.
- Both command-line and graphical user interface versions are available for accessibility.
