@inproceedings{BKL99b,
  author       = {Boghossian, N. P. and Kohlbacher, O. and Lenhof, H.-P.}, 
  editor       = {Vitter, J. S. and Zaroliagis, C. D.},
  title        = {{BALL}: {B}iochemical {A}lgorithms {L}ibrary},
  booktitle    = {Algorithm Engineering, 3rd International Workshop, {WAE}'99,
                  Proceedings},
  series       = {Lecture Notes in Computer Science (LNCS)},
  publisher    = {Springer},
  pages        = {330--344},
  year         = {1999},
  volume       = {1668},
}

@inproceedings{KL99,
  author       = {Kohlbacher, O. and Lenhof, H.-P.}, 
  editor       = {},
  title        = {Rapid Software Prototyping in Computational Molecular
                  Biology},
  booktitle    = {Proceedings of the German Conference on Bioinformatics 
                  ({GCB}'99)},
  pages        = {},
  year         = {1999}
}

@techreport{BKL99a,
  author       = {Boghossian, N. P. and Kohlbacher, O. and Lenhof, H.-P.}, 
  title        = {{BALL}: {B}iochemical {A}lgorithms {L}ibrary},
  address      = {Saar\-br{\"u}cken},
  year         = {1999},
  volume       = {99-1-002},
  institution  = {Max-Planck-Institut f{\"u}r Informatik},
  location     = {MPI-ZB},
  idnumber     = {MPI-I-B-TR7144},
  signature    = {Reports: Saarbr{\"u}cken},
  ISBN         = {0946-011X},
  status       = {available},
  type         = {{R}esearch report},
  bibtype      = {techreport},
}

@article{KL2000,
  author       = {Oliver Kohlbacher and Hans-Peter Lenhof},
  title        = {{BALL} -- rapid software prototyping in computational
                  molecular biology},
  journal      = {Bioinformatics},
  year         = {2000},
  pages        = {815--824},
  volume       = {16},
  number       = {9},
}

@article{MHLK05,
  author       = {Moll, A. and Hildebrandt, A. and Lenhof, A.
                  and Kohlbacher, O.},
  title        = {{BALLView}: {An} object-oriented molecular visualization and
                  modeling framework},
  journal      = {J. Comput.-Aided Mol. Des.},
  year         = {2005},
  pages        = {791--800},
  volume       = {19},
  number       = {11},
}

@article{MHLK06,
  author       = {Moll, A. and Hildebrandt, A. and Lenhof, A. 
                  and Kohlbacher, O.},
  title        = {{BALLView}: {A} tool for research and education in molecular
                  moedling},
  journal      = {Bioinformatics},
  year         = {2006},
  pages        = {365--366},
  volume       = {22},
  number       = {3},
}

@incollection{Koh2001,
  author       = {Kohlbacher, Oliver},
  title        = {{BALL} -- {A} {F}ramework for {R}apid {A}pplication 
                  {D}evelopment in {M}olecular {M}odeling},
  editors      = {Theo Plesser and Helmut Hayd},
  publisher    = {Gesellschaft f{\"u}r wissenschaftliche Datenverarbeitung mbH},
  address      = {G{\"o}ttingen},
  booktitle    = {Beitr{\"a}ge zum Heinz-Billing-Preis 2000},
  number       = {56},
  series       = {Forschung und wissenschaftliches Rechnen - {GWDG} Berichte},
  year         = {2001},
  pages        = {13--30},
}

@misc{BALL-RM,
  key          = {BALL Reference Manual},
  title        = {{BALL} {R}eference {M}anual},
  howpublished = {{\tt http://www.ball-project.org/Do\-cu\-men\-ta\-tion}},
  year         = {2009},
}
	
@article{PDB,
  author       = {Berman, H. M. and Westbrook, J. and Feng, Z.
                  and Gilliland, G. and Bhat, T. N. and Weissig, H.
                  and Shindylov, I. N. and Bourne, P. E.},
  title        = {The {P}rotein {D}ata {B}ank},
  journal      = {Nucleic Acids Res.},
  volume       = {28},
  number       = {1},
  year         = {2000},
  pages        = {235--242}
}

@article{AMBER95,
  author       = {Wendy D. Cornell and Piotr Cieplak and Christopher I. Bayly
                  and Ian R. Gould and {Merz Jr.}, Kenneth M.
                  and David M. Ferguson and David C. Spellmeyer and Thomas Fox
                  and James W. Caldwell and Peter A. Kollman},
  title        = {A Second Generation Force Field for the Simulation of
                  Proteins, Nucleic Acids and Organic Molecules},
  journal      = {J. Am. Chem. Soc.},
  pages        = {5179-5197},
  year         = {1995},
  volume       = {117},
  number       = {19}
}

@article{BBO+83,
  author       = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson
                  and D. J. States and S. Swaminathan and M. Karplus},
  title        = {{CHARMM}: {A} program for macromolecular energy,
                  minimization, and dynamics calculations},
  journal      = {J. Comput. Chem.},
  volume       = {4},
  number       = {2},
  year         = {1983},
  pages        = {187--217}
}

@article{MMFF94a,
  author       = {Halgren, Thomas A.},
  title        = {{Merck} molecular force field. {I}. {B}asis, form, scope,
                  parameterization, and performance of {MMFF94}},
  journal      = {J. Comput. Chem.},
  volume       = {17},
  number       = {5--6},
  pages        = {490--519},
  year         = {1996}
}

@article{MMFF94b,
  author       = {Halgren, Thomas A.},
  title        = {{Merck} molecular force field. {II}. {MMFF94} van der {Waals}
                  and electrostatic parameters for intermolecular interactions},
  journal      = {J. Comput. Chem.},
  volume       = {17},
  number       = {5--6},
  pages        = {520--552}, 
  year         = {1996}
}

@article{MMFF94c,
  author       = {Halgren, Thomas A.},
  title        = {{Merck} molecular force field. {III}. {Molecular} geometries
                  and vibrational frequencies for {MMFF94}},
  journal      = {J. Comput. Chem.},
  volume       = {17},
  number       = {5--6},
  pages        = {553--586}, 
  year         = {1996}
}

@article{MMFF94d,
  author       = {Halgren, Thomas A. and Nachbar, Robert B.},
  title        = {{Merck} molecular force field. {IV}. {Conformational}
                  energies and geometries for {MMFF94}},
  journal      = {J. Comput. Chem.},
  volume       = {17},
  number       = {5--6},
  pages        = {587--615}, 
  year         = {1996}
}

@article{MMFF94e,
  author       = {Halgren, Thomas A.},
  title        = {{Merck} molecular force field. {V}. {Extension} of {MMFF94}
                  using experimental data, additional computational data, and
                  empirical rules},
  journal      = {J. Comput. Chem.},
  volume       = {17},
  number       = {5--6},
  pages        = {616--641},
  year         = {1996}
}

@article{ZVC+97,
  author       = {C. Zhang and G. Vasmatzis and J. L. Cornette and C. DeLisi},
  title        = {Determination of Atomic Desolvation Energies From the
                  Structures of Crystallized Proteins},
  journal      = {J. Mol. Biol.},
  pages        = {707-726},
  year         = {1997},
  volume       = {267},
  number       = {3}
}

@Misc{QT,
  title        = {{Qt} release 4.5},
  howpublished = {{Troll~Tech~ASA}},
  note         = {{\tt http://qt.nokia.com/products/}},
  key          = {QT},
}

 
@Booklet{HyperChem,
  key          = {{HyperChem}},
  title        = {{HyperChem} Release 4.5},
  howpublished = {Hypercube Inc.},
  year         = {1995},
}

@BOOK{DesignPatterns,
  author       = {Gamma, Erich and Helm, Richard and Johnson, Ralph
                  and Vlissides, John},
  title        = {Design patterns: {E}lements of reusable object-oriented
                  software},
  publisher    = {Addison-Wesley},
  address      = {Reading, MA},
  year         = {1995},
  ISBN         = {0-201-63361-2},
}

@misc{OpenGL,
  key          = {OpenGL},
  title        = {{OpenGL} {API} Documentation Overview},
  howpublished = {{\tt http://www.opengl.org/do\-cu\-men\-tation}},
}

@misc{Mesa,
  key          = {Mesa},
  title        = {The {Mesa} {3D} Graphics Library},
  howpublished = {{\tt http://www.mesa3d.org/}},
}

@Misc{SIP,
  author       = {Thompson, Phil},
  title        = {{SIP}: {A} Tool for Generating Python Bindings for {C} and
                  {C}++ Libraries, version 4.7.9},
  year         = {2009},
  howpublished = {{\tt http://www.riverbankcomputing.co.uk/software/sip/}},
}

@Misc{FFTW,
  author       = {Frigo, Matteo and Johnson, Steven G.},
  title        = {{FFTW}: {T}he {F}astest {F}ourier {T}ransform in the {W}est,
                  version 3.1.2},
  year         = {2006},
  howpublished = {{\tt http://www.fftw.org}},
}

@Misc{Python,
  author       = {van Rossum, Guido},
  title        = {Python, version 2.6},
  year         = {2009},
  howpublished = {{\tt http://www.python.org}},
}

@Misc{boost,
  author       = {{The Boost developers}},
  title        = {Boost C++ Libraries, version 1.35},
  year         = {2008},
  howpublished = {{\tt http://www.boost.org/}},
}
