In the first place, 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.

Next we wish to thank the authors of the two pieces of software that Open3DALIGN uses to carry out conformational searches and molecular alignment, that is TINKER and Pharao respectively. So, big thanks to Prof. Jay Ponder for his kind and prompt feedback and for allowing us to include four programs of the TINKER suite (namely, analyze, dynamic, minimize and optimize) in Open3DALIGN. Thanks also to all Pharao developers at Silicos and particularly to Gert Thijs with whom we had some nice discussions.

Finally, we wish to cite the authors of some algorithms which either inspired those implemented in Open3DALIGN [1,2,3], or were implemented exactly as in their original formulation [4,5]:

Program testing has been carried out taking advantage of the ShareGrid distributed platform [6].


  1. Petitjean, M. Computers Chem. 1998, 22, 463-465.   DOI
  2. Richmond, N. J.; Willett, P.; Clark, R. D. J. Mol. Graph. Model. 2004, 23, 199-209.   DOI
  3. Stewart, D. E.; Leyk, Z. The Meschach library
  4. Matsumoto, M.; Nishimura, T. ACM Trans. Model. Comput. Simul. 1998, 8, 3-30.   DOI
  5. Jonker, R.; Volgenant, A. Computing 1987, 38, 325-340.   DOI
  6. 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