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First-Principles Molecular Structure Search with a Genetic Algorithm.

Publication ,  Journal Article
Supady, A; Blum, V; Baldauf, C
Published in: Journal of chemical information and modeling
November 2015

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of the search is not only to find the global minimum but to predict all conformers within an energy window above the global minimum. The performance of the search strategy is (i) evaluated for a reference data set extracted from a database with amino acid dipeptide conformers obtained by an extensive combined force field and first-principles search and (ii) compared to the performance of a systematic search and a random conformer generator for the example of a drug-like ligand with 43 atoms, 8 rotatable bonds, and 1 cis/trans bond.

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Published In

Journal of chemical information and modeling

DOI

EISSN

1549-960X

ISSN

1549-9596

Publication Date

November 2015

Volume

55

Issue

11

Start / End Page

2338 / 2348

Related Subject Headings

  • Thermodynamics
  • Mycophenolic Acid
  • Molecular Conformation
  • Models, Molecular
  • Medicinal & Biomolecular Chemistry
  • Ligands
  • Drug Discovery
  • Drug Design
  • Dipeptides
  • Algorithms
 

Citation

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Supady, A., Blum, V., & Baldauf, C. (2015). First-Principles Molecular Structure Search with a Genetic Algorithm. Journal of Chemical Information and Modeling, 55(11), 2338–2348. https://doi.org/10.1021/acs.jcim.5b00243
Supady, Adriana, Volker Blum, and Carsten Baldauf. “First-Principles Molecular Structure Search with a Genetic Algorithm.Journal of Chemical Information and Modeling 55, no. 11 (November 2015): 2338–48. https://doi.org/10.1021/acs.jcim.5b00243.
Supady A, Blum V, Baldauf C. First-Principles Molecular Structure Search with a Genetic Algorithm. Journal of chemical information and modeling. 2015 Nov;55(11):2338–48.
Supady, Adriana, et al. “First-Principles Molecular Structure Search with a Genetic Algorithm.Journal of Chemical Information and Modeling, vol. 55, no. 11, Nov. 2015, pp. 2338–48. Epmc, doi:10.1021/acs.jcim.5b00243.
Supady A, Blum V, Baldauf C. First-Principles Molecular Structure Search with a Genetic Algorithm. Journal of chemical information and modeling. 2015 Nov;55(11):2338–2348.
Journal cover image

Published In

Journal of chemical information and modeling

DOI

EISSN

1549-960X

ISSN

1549-9596

Publication Date

November 2015

Volume

55

Issue

11

Start / End Page

2338 / 2348

Related Subject Headings

  • Thermodynamics
  • Mycophenolic Acid
  • Molecular Conformation
  • Models, Molecular
  • Medicinal & Biomolecular Chemistry
  • Ligands
  • Drug Discovery
  • Drug Design
  • Dipeptides
  • Algorithms