Towards consistency in geometry restraints for carbohydrates in the pyranose form: Modern dictionary generators reviewed

Robbie P. Joosten, Robert A. Nicholls, Jon Agirre

Research output: Contribution to journalArticlepeer-review

Abstract

Macromolecular restrained refinement is nowadays the most used method for improving the agreement between an atomic structural model and experimental data. Restraint dictionaries, a key tool behind the success of the method, allow fine-tuning geometric properties such as distances and angles between atoms beyond simplistic expectations. Dictionary generators can provide restraint target estimates derived from different sources, from fully theoretical to experimental and any combination in between. Carbohydrates are stereochemically complex biomolecules and, in their pyranose form, have clear conformational preferences. As such, they pose unique problems to dictionary generators and in the course of this study, require special attention from software developers. Functional differences between restraint generators will be discussed, as well as the process of achieving consistent results with different software designs. The study will conclude a set of practical considerations, as well as recommendations for the generation of new restraint dictionaries, using the improved software alternatives discussed.

Original languageEnglish
Pages (from-to)1193-1207
Number of pages15
JournalCurrent Medicinal Chemistry
Volume29
Issue number7
Early online date2 Sep 2021
DOIs
Publication statusPublished - 2022

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Keywords

  • dictionaries
  • Geometry restraints
  • pyranose
  • refinement
  • ring conformation
  • structural biology

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