Open AccessTowards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed
Author(s) -
Robbie P. Joosten,
Robert A. Nicholls,
Jon Agirre
Publication year - 2022
Publication title -
current medicinal chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.934
H-Index - 174
eISSN - 1875-533X
pISSN - 0929-8673
DOI - 10.2174/0929867328666210902140754
Subject(s) - pyranose , consistency (knowledge bases) , set (abstract data type) , computer science , software , key (lock) , process (computing) , algorithm , artificial intelligence , chemistry , programming language , stereochemistry , computer security
: Macromolecular restrained refinement is nowadays the most used method forimproving the agreement between an atomic structural model and experimental data. Restraintdictionaries, a key tool behind the success of the method, allow fine-tuning geometricproperties such as distances and angles between atoms beyond simplistic expectations.Dictionary generators can provide restraint target estimates derived from differentsources, from fully theoretical to experimental and any combination in between. Carbohydratesare stereochemically complex biomolecules and, in their pyranose form, haveclear conformational preferences. As such, they pose unique problems to dictionary generatorsand in the course of this study, require special attention from software developers.Functional differences between restraint generators will be discussed, as well as the processof achieving consistent results with different software designs. The study will concludea set of practical considerations, as well as recommendations for the generation ofnew restraint dictionaries, using the improved software alternatives discussed.