Publications

  • Smadbeck J., Peterson M.B., Khoury G.A., Taylor M.S., and Floudas C.A., "Protein WISDOM: a workbench for in silico de novo design of biomolecules." J Vis Exp (2013).

  • Bellows M.L., Taylor M.S., Cole P.A., Shen L., Siliciano R.F., Fung H.K., and Floudas C.A., "Discovery of entry inhibitors for HIV-1 via a novel de novo protein design framework", Biophysical J., 99, 3445-3453 (2010).

  • Bellows M.L., Fung H.K., Taylor M.S., Floudas C.A., Lopez de Victoria A. and D. Morikis, "New Compstatin Variants Through Two De Novo Protein Design Frameworks", Biophysical J., 98, 2337-2346 (2010).

  • Bellows M.L., Fung H.K., and C.A. Floudas., "Recent Advances In De Novo Protein Design", Chapter in Process Systems Engineering: Vol. 6 Molecular Systems Engineering, Eds. C.S. Adjiman and A. Galindo, Wiley-VCH, 207-232 (2010).

  • Bellows M.L. and C.A. Floudas, "Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7 and histone demethylases", Current Drug Targets, 11, 264-278 (2010).

  • Sun J., Abdeljabbar D.M., Clarke N., Bellows M.L., Floudas C.A., and A.J. Link, "Reconstitution and Engineering of Apoptotic Protein Interactions on the Bacterial Cell Surface", J. Molecular Biology, 394, 297-305 (2009).

  • Floudas C.A, Fung H.K., Morikis D., Taylor M.S., and L. Zhang, "Overcoming the Key Challenges in De Novo Protein Design: Enhancing Computational Efficiency and Incorporating True Backbone Flexibility", Proceedings of BIOMAT VI, Ed. R. Mondaini, Springer, 102, 133-183 (2008).

  • Fung H.K., Welsh W.J., and C.A. Floudas, "Computational De Novo Peptide and Protein Design: Rigid Templates versus Flexible Templates", IECR, 47, 993-1001 (2008).

  • Fung H.K., Floudas C.A, Taylor M.S., Zhang L., and D. Morikis, "Towards Full Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2", Biophysical J., 94, 584-599 (2008).

  • Taylor M.S., Fung H.K., Rajgaria R., Filizola M., Weinstein H., and C.A. Floudas, "Mutations Affecting the Oligomerization Interface of G-Protein Coupled Receptors Revealed by a Novel De Novo Protein Design Framework", Biophysical J., 94, 2470-2481 (2008).

  • Fung H.K., Taylor M.S. and C.A. Floudas, "Novel Formulations for the Sequence Selection Problem in de Novo Protein Design with Flexible Templates", Optimization Methods and Software, 22 (1), 51-71 (2007).

  • Floudas C.A. and H.K. Fung, "Mathematical Modeling and Optimization Methods for De Novo Protein Design", in Systems Biology, I. Rigoutsos and G. Stephanopoulos (Eds), Oxford University Press, 42-66, (2007).

  • Floudas C.A., H.K. Fung, S.R. McAllister, M. Monnigmann, and R. Rajgaria, "Advances in Protein Structure Prediction and De Novo Protein Design: A Review", Chemical Engineering Science, 61, 966-988 (2006).

  • Fung H.K., Rao S., Floudas C.A., Prokopyev O., Pardalos P.M., and F. Rendl, "Computational Comparison Studies of Quadratic Assignment Like Formulations for the In Silico Sequence Selection Problem in De Novo Protein Design", Journal of Combinatorial Optimization, 10, 41-60 (2005).

  • Klepeis J.L. and C.A. Floudas, "In silico design of peptides and proteins: A combinatorial and global optimization approach", SIAM news (2004).

  • Floudas C.A. and J.L. Klepeis and J.D. Lambris and D. Morikis, "De novo protein design: An interplay of global optimization, mixed-integer optimization, and experiments", Proceedings of FOCAPD'2004, eds. C.A. Floudas and A. Agrawal, pp. 133-146 (2004).

  • Klepeis J.L., C.A. Floudas, D. Morikis, and J.D. Lambris, "Design of Peptide Analogs with Improved Activity using a Novel de novo Protein Design Approach", Industrial and Engineering Chemistry Research, 43, 3817-3826 (2004).

  • Morikis D., A.M. Soulika, B. Mallik, J.L. Klepeis, C.A. Floudas, and J.D. Lambris, "Improvement of the anti-C3 activity of complement using rational and combinatorial approaches", Biochemical Society Transactions, 32, 28-32 (2003).

  • Klepeis J.L., C.A. Floudas, D. Morikis, C.G. Tsokos, E. Argyropoulos, L. Spruce, and J.D. Lambris, "Integrated Computational and Experimenal Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity", Journal of the American Chemical Society, 125 (28), 8422-8423 (2003).