List of software and web servers used for structure optimization of molecules

  • Ballon Balloon generates 3D atomic coordinates using molecular connectivity via distance geometry. It uses multiobjective genetic algorithm for generating of 3D conformers.
  • MOPAC Molecular Orbital PACkage (MOPAC) is an open source semi-empirical quantum chemistry program that is used to study molecular structures and reactions. molecular orbital package.
  • Openbabel Openbabel is a free software, used in the inter-conversion of chemical structure/conformers (2D/3D) and different chemical file formats, substructure search, force field calculation, extraction of stereochemical information and fingerprint calculation.
  • Frog FROG identifies the different unambiguous isomers corresponding to each molecule.
  • DG-AMMOS DG-AMMOS is an open-source program, which allows the generation of the 3D conformation of small molecules using distance geometry and their energy minimization.
  • SMI23D Smi23d (3D Coordinate Generation) program converts one or more SMILIES strings into 3D.
  • Cyndi Cyndi is fast and powerful structure conformation generation package based on the multiobjective evolution algorithm capable of generating geometrically diverse conformers at the large scale.
  • TINKER TINKER is a widely used molecular modeling software having several features such as molecular dynamics, minimization and conformational sampling.