How the methodology of 3D structure preparation influences the quality of QSPR models?
QSPR modelling is a very useful and popular methodology for estimating the physical and chemical properties of molecules. The inputs for QSPR models are 3D structures of molecules. Currently, the 3D structures for millions of molecules are publicly available. A large number of these 3D structures were generated by software tools for the conversion of 2D structures into 3D. Moreover, the generated structures can be geometrically optimized by different approaches, such as molecular mechanics, quantum mechanics, etc.. The question arises as to how the methodology of 3D structure preparation influences the quality of QSPR models that use these structures. Is there some software tool for 3D structure construction more suitable for QSPR modelling purposes than others? Conversely, which software tools are inappropriate? How strong is the influence of the geometry optimization procedure? We focused on these questions in the present study.
In our work, we analyzed the influence of 3D structure p ...
- Svobodová Vařeková R, Geidl S, Ionescu CM, Skřehota O, Kudera M, Sehnal D, Bouchal T, Abagyan R, Huber JH, Koča J: Predicting pK a values of substituted phenols from atomic charges. J Chem Inf Model 2011, 51:1795–1806. CrossRef
- Sadowski J, Gasteiger J: From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders. Chem Rev 1993, 93:2567–2581. CrossRef
- Vainio MJ, Johnson MS: Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model 2007, 47:2462–2474. CrossRef
- How the methodology of 3D structure preparation influences the quality of QSPR models?
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
Journal of Cheminformatics
- Online Date
- May 2012
- Online ISSN
- Chemistry Central
- Additional Links
- Author Affiliations
- 1. National Centre for Biomolecular Research and CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, CZ, Czech Republic