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Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility. (English) Zbl 1382.92209
Mondaini, Rubem P. (ed.) et al., Mathematical modelling of biosystems. Berlin: Springer (ISBN 978-3-540-76783-1/hbk). Applied Optimization 102, 133-183 (2008).
Summary: De novo protein design is initiated with a postulated or known flexible threedimensional protein structure and aims at identifying amino acid sequences compatible with such a structure. The problem was first denoted as the “inverse folding problem” [K. E. Drexler, “Molecular engineering: an approach to the development of general capabilities for molecular manipulation”, Proc. Natl. Acad. Sci. 78, No. 9, 5275–5278 (1981; doi:10.1073/pnas.78.9.5275); C. Pabo, “Molecular technology: designing proteins and peptides”, Nature 301, 200 (1983; doi:10.1038/301200a0)] since protein design has intimate links to the well-known protein folding problem [C. Hardin et al., “Ab initio protein structure prediction”, Curr. Opinion Struct. Biol. 12, No. 2, 176–181 (2002; doi:10.1016/s0959-440x(02)00306-8)]. While the protein folding problem aims at determining the single structure for a sequence, the de novo protein design problem exhibits a high level of degeneracy; that is, a large number of sequences are always found to share a common fold, although the sequences will vary with respect to properties such as activity and stability.
For the entire collection see [Zbl 1134.92001].
MSC:
92D20 Protein sequences, DNA sequences
92-08 Computational methods for problems pertaining to biology
Software:
TINKER; DYANA; CPLEX; CYANA
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References:
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