# Credits

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]:

- M. Petitjean for his description of the combined SDM/RMS algorithm
[1]

- N. J. Richmond, P. Willett, R. D. Clark for the description of their LAMDA algorithm
[2]

- D. E. Stewart and Z. Leyk, for providing inspiration with their
Meschach
library about how to code an efficient quicksort
routine [3]

- R. Jonker and A. Volgenant for their "Shortest Augmenting Path Algorithm
for Dense and Sparse Linear Assignment Problems" [5]

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

#### REFERENCES

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