TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

Journal of Cheminformatics

Irea Mosquera-Lois¹  David Ferro-Costas¹  Antonio Fernández-Ramos¹ 

[1] Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain;

关键词: Conformations;    Flexible molecules;    Torsions;    Preconditioned search;    Stochastic search;    Validation tests;    Amino acids;   

DOI  :  10.1186/s13321-021-00578-0

来源: Springer

【 摘 要 】

In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.Graphical Abstract

【 授权许可】

CC BY