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The software is provided without warranty of any kind.
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Proteus documentation (preliminary)
XPLOR 3.8 with local modifications
The two main references for Proteus are:
T. Simonson, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart & G. Archontis (2013) Journal of Computational Chemistry, in press, 0000. Computational protein design: the Proteus software and selected applications
M. Schmidt am Busch, A. Lopes, D. Mignon & T. Simonson (2008) Journal of Computational Chemistry, 29, 1092-1102. Computational protein design: software implementation, parameter optimization, and performance of a simple method
Other related publications from our lab
S. Polydorides & T. Simonson (2013) Journal of Computational Chemistry , in press, 0000. Monte Carlo simulations of proteins at constant pH with generalized Born solvent.
T. Simonson (2013) Journal of Chemical Theory and Computation , in press, 0000. What is the dielectric constant of a protein when its backbone is fixed?
T. Simonson (2013) Current Pharmaceutical Design, 19, 4241-56. Protein:ligand recognition: simple models for electrostatic effects.
M. Schmidt am Busch, A. Lopes, D. Mignon, T. Gaillard & T. Simonson (2012) In Quantum Simulations of Materials and Biological Systems (editors: J. Zeng, R. Zhang, H. Treutlein), Springer Verlag, New York. Pages 121-140. The inverse protein folding problem: protein design and structure prediction in the genomic era.
S. Polydorides, N. Amara, T. Simonson & G. Archontis (2011) Proteins, 79, 3448-3468. Computational protein design with a generalized Born solvent model: application to asparaginyl-tRNA synthetase.
A. Aleksandrov, S. Polydorides, G. Archontis & T. Simonson (2010) Journal of Physical Chemistry B, 114, 10634-10648. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized Born solvent.
M. Schmidt am Busch, A. Sedano & T. Simonson (2010) Plos One, 5(5), e10410. Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.
A. Lopes, M. Schmidt am Busch & T. Simonson (2010) Journal of Computational Chemistry, 31, 1273-1286. Computational design of protein:ligand binding: modifying the specificity of asparaginyl-tRNA synthetase.
M. Schmidt am Busch, D. Mignon & T. Simonson (2009) Proteins, 77, 139â158. Computational protein design as a tool for fold recognition.
J. Noirel & T. Simonson (2008) Journal of Chemical Physics, 129, 185104-185112. Neutral evolution of proteins: the superfunnel in sequence space and its relation to mutational robustness.
M. Schmidt am Busch, A. Lopes, N. Amara, C. Bathelt & T. Simonson (2008) BMC Bioinformatics, 9, 148-163. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.
J. Noirel & T. Simonson (2007) BMC Structural Biology, 7, 79-93. Neutral evolution of protein-protein interactions: a computational study using simple models.
A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis & T. Simonson (2007) Proteins, 67, 853-867. Computational sidechain placement and protein mutagenesis with implicit solvent models.
G. Archontis & T. Simonson (2005) Journal of Physical Chemistry B, 109, 22667-22673. A residue-pairwise Generalized Born model suitable for protein design calculations.