Joosten, Robbie P., Nicholls, Robert A. and Agirre, Jon orcid.org/0000-0002-1086-0253 (2022) Towards consistency in geometry restraints for carbohydrates in the pyranose form:Modern dictionary generators reviewed. Current Medicinal Chemistry. pp. 1193-1207. ISSN 1875-533X
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2021 Bentham Science Publishers. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details. |
Keywords: | dictionaries,Geometry restraints,pyranose,refinement,ring conformation,structural biology |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Chemistry (York) |
Depositing User: | Pure (York) |
Date Deposited: | 29 Nov 2021 14:10 |
Last Modified: | 16 Oct 2024 18:02 |
Published Version: | https://doi.org/10.2174/0929867328666210902140754 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.2174/0929867328666210902140754 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:181015 |
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Filename: Current_Medicinal_Chemistry_dictionaries_draft_2.pdf
Description: Current Medicinal Chemistry - dictionaries draft-2