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Current Medicinal Chemistry

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Review Article

Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed

Author(s): Robbie P. Joosten, Robert A. Nicholls and Jon Agirre*

Volume 29, Issue 7, 2022

Published on: 02 September, 2021

Page: [1193 - 1207] Pages: 15

DOI: 10.2174/0929867328666210902140754

open access plus

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.

Keywords: Geometry restraints, ring conformation, pyranose, structural biology, dictionaries, refinement.

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