ArticleJournal of cheminformatics2021
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids.
Article in Journal of cheminformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Designing Molecular Solar Thermal Systems Based on the Paternò-Büchi Reaction Coupled to Enzymatic Energy Release.ChemSusChem · 2025Article
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- Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation.Journal of chemical information and modeling · 2024Article
- Combined DFT and Kinetic Monte Carlo Study of UiO-66 Catalysts for γ-Valerolactone Production.The journal of physical chemistry. C, Nanomaterials and interfaces · 2024Article
- DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline.The journal of physical chemistry. A · 2023Article
- Toward Spectroscopic Accuracy for the Structures of Large Molecules at DFT Cost: Refinement and Extension of the Nano-LEGO Approach.The journal of physical chemistry. A · 2023Article
- Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods.The journal of physical chemistry. A · 2023Article
- Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy.Journal of chemical theory and computation · 2023Article
- Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks.Molecules (Basel, Switzerland) · 2023Article
- Benchmark Ab Initio Determination of the Conformers, Proton Affinities, and Gas-Phase Basicities of Cysteine.The journal of physical chemistry. A · 2022Article
- New Multifunctional Agents for Potential Alzheimer's Disease Treatment Based on Tacrine Conjugates with 2-Arylhydrazinylidene-1,3-Diketones.Biomolecules · 2022Article
- Molecular Conformer Search with Low-Energy Latent Space.Journal of chemical theory and computation · 2022Article
- Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids.Journal of cheminformatics · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
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.
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