A survey of computational tools for heterochiral proteins

Abstract Protein structures that, unlike those currently ubiquitous in the biological world, involve comparable quantities of l - and d -amino acids have impact on drug development and even on the study of the origin of life. Predictable l and d alternations, of which Gramicidin A provides an example, and heterochiral multi-domain structures with homochiral subunits are central in this field. In this work, a practical evaluation is made of computational tools that are available for the modeling of such structures. The tools considered here are generative grammars, l -systems, molecular rendering, generative symmetry, optimization by force field, and ab initio methods. Test case structures are used to illustrate each tool. Graphical Abstract