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SDF2XYZ2SDF: how to exploit TINKER power in cheminformatics projects.

Paolo Tosco¹, Thomas Balle, Fereshteh Shiri

¹Department of Drug Science, University of Torino, Via Pietro Giuria 9, 10125 Torino, Italy. paolo.tosco@unito.it

Journal of Molecular Modeling

|May 17, 2011

Summary

An open-source tool, SDF2XYZ2SDF, converts chemical files into formats usable by TINKER molecular mechanics software. This integration enhances automated cheminformatics workflows, including virtual screening and conformational searches.

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Area of Science:

Computational chemistry
Cheminformatics

Background:

Molecular mechanics (MM) computations are crucial for understanding molecular behavior.
Integrating MM into automated workflows requires compatible file formats.
Existing tools may lack flexibility in file conversion for specific MM packages.

Purpose of the Study:

To introduce SDF2XYZ2SDF, an open-source tool for converting chemical file formats.
To enable the use of TINKER molecular mechanics computations within automated cheminformatics pipelines.
To facilitate advanced computational tasks such as conformational searches and virtual screening.

Main Methods:

Development of an open-source software tool, SDF2XYZ2SDF.
Leveraging OpenBabel for broad file format compatibility.

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Conversion of Structure-Data files (SDF) and other formats to MMFF-typed XYZ coordinate files.

Integration with the TINKER molecular mechanics software package.

Main Results:

Successful conversion of SD files and other formats to TINKER-compatible XYZ files.
Demonstrated utility of SDF2XYZ2SDF in automating the preparation of input files for molecular mechanics.
Enabled seamless integration of TINKER computations into cheminformatics workflows.

Conclusions:

SDF2XYZ2SDF provides a valuable bridge between diverse chemical file formats and the TINKER MM package.
The tool enhances the efficiency and scope of automated cheminformatics tasks.
Facilitates broader adoption of robust molecular mechanics calculations in research.