Computer-aided design of amino acid-based therapeutics: a review

Farhadi, Tayebeh; Hashemian, Seyed MohammadReza

Overall, in silico design of amino acid-based therapeutics includes many challenges that should be removed to improve the overall performance of the design processes. For example, although structure determination of all disease-related proteins through crystallography and NMR is a laborious task, it is necessary to gather much structural information of peptide-protein interactions. Besides, development of vigorous algorithms to calculate protein-protein binding energies is essential. The estimation of binding constant between two macromolecules with an appropriate speedaccuracy tradeoff needs millisecond scale molecular dynamics. Moreover, understanding of both protein-protein and protein-peptidomimetics recognition processes in a molecular level can be improved using higher accurate force fields such as quantum mechanical polarizable force.