In the first place, we wish to state that Open3DQSAR would never have seen the light of day without the invaluable pioneering work of Prof. Gabriele Cruciani and colleagues in the field of chemometrics applied to 3D-QSAR. We have referred to their detailed published methodologies [1, 2, 3, 4] to code Open3DQSAR's implementation of the Smart Region Definition and Fractional Factorial Design algorithms, a task which would have been extremely hard in the absence of such outstanding guidance.

Next we wish to acknowledge the contribution to our project of OpenBabel, which allowed to speed up the development of the atom typing code; thanks to all OpenBabel developers and in particular to Geoffrey Hutchison, who merged in real time our changes and additions to the OpenBabel development trunk.

We are also indebted to the authors of the UVE-PLS and IVE-PLS methodologies, as well as to the authors of their later extensions [5, 6, 7]. Progressive scrambling was implemented according to the original work published by Clark and Fox [8].

Finally, we wish to cite the authors of some algorithms we used in Open3DQSAR, and namely:

Program testing has been carried out taking advantage of the ShareGrid distributed platform [11]


  1. Baroni, M.; Costantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Quant. Struct-Act. Relat. 1993, 12, 9-20.   DOI
  2. Baroni, M.; Clementi, S.; Cruciani, G.; Costantino, G.; Riganelli, D. J. Chemometr. 1992, 6, 347-356.   DOI
  3. Kastenholz, M. A.; Pastor, M.; Cruciani, G.; Haaksma, E. E. J.; Fox, T. J. Med. Chem. 2000, 43, 3033-3044.   DOI
  4. Pastor, M.; Cruciani, G.; Clementi, S. J. Med. Chem. 1997, 40, 1455-1464.   DOI
  5. Centner, V.; Massart, D. L.; de Noord, O. E.; de Jong, S.; Vandeginste, B. M.; Sterna, C. Anal. Chem. 1996, 68, 3851-3858.   DOI
  6. Gieleciak, R.; Polanski, J. J. Chem. Inf. Model. 2007, 47, 547-556.   DOI
  7. Grohmann, R.; Schindler, T. J. Comput. Chem. 2008, 29, 847-860.   DOI
  8. Clark, R. D.; Fox, P. C. J. Comput.-Aided Mol. Des. 2004, 18, 563-576.   DOI
  9. Lekien, F.; Marsden, J. Int. J. Numer. Methods Eng. 2005, 63, 455-471.   DOI
  10. Matsumoto, M.; Nishimura, T. ACM Trans. Model. Comput. Simul. 1998, 8, 3-30.   DOI
  11. Anglano, C.; Canonico, M.; Guazzone, M.; Botta, M.; Rabellino, S.; Arena, S.; Girardi, G. Proceedings of CCGRID'08, May 2008, Lyon (France), IEEE Press.   DOI

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