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Abstract
In this paper, we propose to use parametrized secondary structure as low-dimensional space during optimization of aptamer sequence. We are testing the efficiency of a simple approach that directly maximizes shape complementarity on the intermolecular interface. From a library of symmetric parametrically designed structures, we identified a ssDNA sequence binding human insulin. Using molecular dynamics, we got an estimation of its binding affinity to be Kd = 6 μM.
Supplementary weblinks
Title
DESIGN OF AN APTAMER BY SHAPE COMPLEMENTARITY MAXIMIZATION FOR INSULIN BINDING
Description
Code used for generation of screening library and for molecular dynamics study using Gromacs.
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