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Tools for ligand validation in Coot.

Paul Emsley1

  • 1MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.

Acta Crystallographica. Section D, Structural Biology
|March 15, 2017
PubMed
Summary
This summary is machine-generated.

Coot now offers new tools for validating and comparing ligands in protein structures. These tools use density-fit, distortion, and atom-clash metrics to assess ligand quality within protein-ligand complexes.

Keywords:
Cootligand manipulationligand representationligand validationmodel building

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Biochemistry

Background:

  • Coot is a widely used molecular graphics program for X-ray crystallography.
  • Recent developments have expanded Coot's capabilities to include ligand manipulation and representation.
  • Assessing the quality of ligands within protein-ligand complexes is crucial for structural biology research.

Purpose of the Study:

  • To describe new tools within Coot for ligand validation and comparison.
  • To introduce metrics for evaluating ligand fit, distortion, and clashes in protein complexes.
  • To enable users to assess the quality of ligands using interactive scoring distributions.

Main Methods:

  • Development and implementation of new ligand validation tools in Coot.
  • Scoring of ligands from the Worldwide Protein Data Bank (wwPDB) using density-fit, distortion, and atom-clash metrics.
  • Utilizing interactive sliders for visualizing and comparing ligand quality scores.

Main Results:

  • Established a scoring system for ligands based on key structural and chemical properties.
  • Demonstrated the utility of density-fit, distortion, and atom-clash metrics for ligand assessment.
  • Provided a user-friendly interface for evaluating ligand quality within protein-ligand complexes.

Conclusions:

  • The new Coot tools enhance the ability to validate and compare ligands in structural models.
  • These tools facilitate the assessment of ligand quality in protein-ligand complexes, aiding researchers.
  • The interactive scoring distributions offer valuable insights for refining structural models.