Tim Vandermeersch

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BACKGROUND A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of(More)
UNLABELLED BACKGROUND The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular(More)
BACKGROUND Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. RESULTS Confab generates conformations using the 'torsion driving approach' which(More)
We present a new program for conformer generation, Confab, which aims to generate diverse low energy conformers that span the space of all possible conformations. Such conformers are required for use in fields such as docking and pharmacophore searching and generation. Confab uses a torsion driving approach to travel through the set of systematically(More)
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