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SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization.

Marine Bugnon1, Mathilde Goullieux1, Ute F Röhrig1

  • 1Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.

Journal of Chemical Information and Modeling
|October 19, 2023
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Summary
This summary is machine-generated.

The updated SwissParam tool simplifies computer-aided drug design by generating molecular mechanics force field parameters for small molecules. It now supports covalent ligands and provides tautomer/protonation state information for enhanced accuracy.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Computer-aided drug design (CADD) accelerates drug discovery.
  • Structure-based approaches rely on biomacromolecular structures.
  • Generating accurate force field parameters for small molecules is a significant challenge.

Purpose of the Study:

  • To present an updated version of the SwissParam web tool.
  • To enhance the generation of molecular mechanics parameters and topologies for small molecules.
  • To improve compatibility with modern molecular dynamics force fields.

Main Methods:

  • Updated SwissParam tool based on Merck molecular force field (MMFF).
  • Compatibility with CHARMM36 force field and CHARMM General Force Field (CGenFF) via MATCH.
  • Support for covalent ligands, various import formats, and a molecular sketcher.

Main Results:

  • Enhanced parameter generation for small molecules in drug design.
  • Support for covalent ligand parametrization.
  • Inclusion of tautomer and protonation state information for comprehensive analysis.

Conclusions:

  • The updated SwissParam tool offers improved capabilities for generating accurate molecular parameters.
  • It facilitates structure-based drug design by addressing challenges in small molecule parametrization.
  • The tool is freely available and accessible via web and command-line interfaces.