FIG. 1.

The upper panels show the tertiary structure of the SIAp1 aptamer–phosphatidylserine (PS) complex generated using visual molecular dynamics (VMD) (Humphrey et al., 2006) and the two-dimensional structure of PS. Adenine is colored by blue and guanine is red. The lower panels plot the relative entropy at each step of the designing process using total (lower left) and interaction (lower right) energy as input information are plotted. The preferred nucleotide type is labeled within the boxes; the numbering beside each nucleotide denotes the connection end. The odd numbers, except for the first step, refer to the nucleotide attachment at the 3′ end of the apatmer and the even numbers are for attachment at the 5′ end.