Motivation: The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A computational investigation to evaluate the relative binding ability of a group of anti- Angiopoietin-2 aptamersis proposed and tested against data already available in the literature. Results: The procedure consists of three steps: a. the production of a large set of conformations for each candidate aptamer ; b. the rigid docking upon the receptor ; c. the topological and electrical characterization of the products. Steps a and b allow a global binding score of the ligand-receptor complexes , based on the distribution of the "effective affinity", i.e. the sum of the conformational and the docking energies . Step c. employes a complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the complexes. Finally, a comparison of the theoretical results with the measurements obtained for the same aptamers in experiments on the SPR biosensor is performed, revealing a good agreement .
 The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A novel strategy is proposed to validate the reliability of the 3D structures of aptamers, produced in silico by using free software. The procedure consists of three steps: a. the production of a large set of conformations for each candidate aptamer , b. the rigid docking upon the receptor , c. the topological and electrical characterization of the products. Steps a . and b. allow a global binding score of the ligand-receptor complexes based on the distribution of the "effective affinity", i.e. the sum of the conformational and the docking energy . Step c. employs a complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the ligand-receptor complexes. The test-bed is represented by a group of anti- Angiopoietin-2 aptamers. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree, while our results show a good agreement with the known measurements. The devised procedure is not aptamer-specific and, integrating structure production with structure selection, candidates itself as a quite complete theoretical approach for aptamer selection .
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Motivation:
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computational investigation to evaluate the relative binding ability of a group of anti- Angiopoietin-2 aptamersis proposed and tested against data already available in the literature. Results:
novel strategy is proposed to validate the reliability of the 3D structures of aptamers, produced in silico by using free software.
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complexes. Finally, a comparison of the theoretical results with the measurements obtained for the same aptamers in experiments on the SPR biosensor is performed, revealing a good agreement
ligand-receptor complexes. The test-bed is represented by a group of anti- Angiopoietin-2 aptamers. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree, while our results show a good agreement with the known measurements. The devised procedure is not aptamer-specific and, integrating structure production with structure selection, candidates itself as a quite complete theoretical approach for aptamer selection