Computational protein design

Jaramillo A, Wodak SJ. Computational protein design is a challenge for implicit solvation models. Biophys J 2005 88 156-71. 

Dantas G, Kuhlman B, Callender D, Wong M, Baker D. A large scale test of computational protein design folding and stability of nine completely redesigned globular proteins. J Mol Biol 2003 332 449-60. 

Park S, Yang X, Saven JG. Advances in computational protein design. Curr Opin Struct Biol 2004 14 487-94. 

Street, A. G., Mayo, S. L., Computational protein design, Structure 1999, 7, R105-R109... 

Protein Thermodynamics Protein Interactions Computational Protein Design Conclusions... 

The applications of the chemistry of amino acids to the biological problem, protein structure and function, and folding and stability are the main focus of this article. The article is divided into hve main sections that include the biological insights on protein structures, chemical applications including protein functions, thermodynamics of proteins, protein interactions, and computational protein design. 

Lippow SM, Tidor B. Progress in computational protein design. Curr. Opin. Biotechnol. 2007 18 305-311. 

Bolon DN, Grant RA, Baker TA, Sauer RT. Specificity versus stability in computational protein design. Proc. Natl. Acad. Sci. U.S.A. 2005 102 12724-12729. 

Schmidt am Busch M, Sedano A, Simonson T (2010) Computational protein design validation and possible relevance as a tool for homology searching and fold recognition. PLoS ONE 5(5) el0410... 

Pleiss J (2011) Protein design in synthetic biology. Curr Opin Biotechnol 22 611-617 Samish 1, Perez-Aguilar JM, Saven JG (2011) Theoretical and computational protein design. Annu Rev Phys Chem 62 129-149... 

Schmidt am Busch M, Lopes A, Mignon D, Simonson T (2008) Computational protein design software implementation, parameter optimization, and performance of a simple model. J Comput Chem 29 1092-1102... 

Vizcarra CL, Zhang NG, Marshall SA, Wingreen NS, Zeng C, Mayo SL (2008) An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J Comput Chem 29 1153-1162... 

X-ray diffraction analysis -> absolute molecular structure. First protein structures combined with powerful computing-> protein design... 

Saven, J.G. (2011) Computational protein design engineering molecular diversity, noimatural enzymes, non-biological cofactor complexes, and membrane proteins. Curr. Opin. Chem. Biol, 15 (3), 452 -457. 

Pantazes, R.J., Grisewood, M.J., and Maranas, C.D. (2011) Recent advances in computational protein design. Curr. Opin. Struct. Biol, 21 (4), 467—472. 

We have recently introduced a combined structural, computational, and experimental approach for the de novo design of novel inhibitors such as variants of the synthetic cyclic peptide Compstatin. A novel two-stage computational protein design method is used not only to select and rank sequences for a particular fold but also to validate the stability of the fold for these selected sequences. To correctly select a sequence compatible with a given backbone template that is flexible and represented by several NMR structures, an appropriate energy function must first be identified. The proposed sequence selection procedure is based on optimizing a pairwise distance-dependent interaction potential. A number of different parameterizations for pairwise residue interaction potentials exist the one employed here is based on the discretization of alpha carbon distances into a set of 13 bins to create a finite number of interactions, the parameters of which were derived from a linear optimization formulated to favor native folds over... 

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