SYLVIA - Estimation of the Synthetic Accessibility of Organic Compounds

SYLVIA

SYLVIA rapidly calculates the synthetic accessibility of organic compounds, i.e., how complex it is to make (synthesize) a molecule in the laboratory. SYLVIA ranks the compounds on a scale from 1 to 10 and can prioritize thousands of molecules, e.g., generated by de novo design experiments or retrieved from large virtual compound libraries, according to their synthetic complexity.

SYLVIA synthetic accessibility ranking

Thus, SYLVIA bridges the areas of computer-aided molecular design, chemoinformatics and synthetic chemistry and supports the Green Chemistry paradigm.

References

[1] Boda K, Seidel T, Gasteiger J. Structure and reaction based evaluation of synthetic accessibility. J. Comp.-Aided Mol. Des. 2007, 21, 311-325.
[2] Bonnet P. Is chemical synthetic accessibility computationally predictable for drug and lead-like molecules? A comparative assessment between medicinal and computational chemists. European Journal of Medicinal Chemistry 2012, 54, 679-689.
[3] Gasteiger J. Cheminformatics: Computing target complexity. Nature Chemistry 2015, 7(8), 619-620.
[4] van Vlijmen H, Desjarlais RL, Mirzadegan T. Computational chemistry at Janssen. J. Comput.-Aided Mol. Des. 2017, 31, 267–273.

Features & Functionality

  • Calculates a synthetic accessibility score of organic compounds on a scale from 1 (straightforward synthesis target) to 10 (complex and challenging synthesis target) based on
    • Structure-based components
      • Molecular graph complexity
      • Ring complexity
      • Stereochemical complexity
    • Starting material-based component: similarity to available chemicals
    • Reaction-based component: frequency analysis on the presence of strategic bonds that are extracted from reaction databases
  • Output of scores of all individual components contributing to the total synthetic accessibility score
  • Handles a broad range of organic chemistry
  • Supports the generation and loading of customized starting material and reaction databases (extension or replacement of built-in databases)
    • Customization towards known in-house chemistry
    • GUI and batch tool to generate customized databases
  • Processes about 4 compounds per second on a 2.0 GHz workstation (batch version)

User Interface

  • Command line interface supporting batch mode
  • Wizard-driven graphical user interface including
    • Visualization of chemical structures, synthetic accessibility scores and read-in information
    • Adjustable color-coding for low, medium and high synthetic accessibility scores
    • Options for sorting and filtering of compounds
    • Structure input via file or by a molecule editor
  • Database Manager for generation and importing of customized starting material and reaction center substructure databases
  • Supports standard chemical file formats such as SD/RDfile and SMILES

Screenshot

screenshot of SYLVIA

System Requirements

  • Microsoft Windows 7/8/10 (win32)

Additional Info

Downloadable PDFs

Slide Show

SYLVIA - Synthetic Accessibility Estimation

Evaluation

A demo version of SYLVIA is available for download in our Download Area (after registration).