How to convert a 2D compound/ structure to 3D for use in molecular...

Commercial tools for generating low-energy conformations: molconvert (ChemAxon), conformational search in MOE.

David Seidman  Follow Following

Commercial tools for generating low-energy conformations: molconvert (ChemAxon), conformational search in MOE.

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Hi, you can convert 2D or 1D (SMILES) molecule file into 3D molecular structures using different ways, such as:
1. Using OpenBabel as a standalone tool, https://sourceforge.net/projects/openbabel/
2. OpenBabel as web-server, http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html (Comparatively easier approach)
3. Using ChemDraw/ MarvinSketch etc.

For energy minimization, you may use
1. Avogadro, https://avogadro.cc/
2. If you perform docking using PyRx/ Glide or some other sophisticated software, they have options for energy minimization before docking.

Watch some YouTube tutorials to get more insights about the tools.

Connie Francisco's Space  Follow Following

Hi, you can convert 2D or 1D (SMILES) molecule file into 3D molecular structures using different ways, such as:
1. Using OpenBabel as a standalone tool, https://sourceforge.net/projects/openbabel/
2. OpenBabel as web-server, http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html (Comparatively easier approach)
3. Using ChemDraw/ MarvinSketch etc.

For energy minimization, you may use
1. Avogadro, https://avogadro.cc/
2. If you perform docking using PyRx/ Glide or some other sophisticated software, they have options for energy minimization before docking.

Watch some YouTube tutorials to get more insights about the tools.

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Upvote

VOTE

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