New indicators for assessing the quality of in silico produced biomolecules: the case study of the aptamer-Angiopoietin-2 complex

TL;DR

This paper introduces a new scoring method for evaluating in silico generated aptamer structures by analyzing their topological and electrical properties, improving the prediction of binding features for biosensor design.

Contribution

A novel procedure combining free docking results with likelihood estimates based on topological and electrical properties for aptamer quality assessment.

Findings

Identified two main conformer types with distinct binding capabilities

The method enhances ranking accuracy of aptamer structures

Applicable to various biomolecules for biosensor development

Abstract

Computational procedures to foresee the 3D structure of aptamers are in continuous progress. They constitute a crucial input to research, mainly when the crystallographic counterpart of the structures in silico produced is not present. At now, many codes are able to perform structure and binding prediction, although their ability in scoring the results remains rather weak. In this paper, we propose a novel procedure to complement the ranking outcomes of free docking code, by applying it to a set of anti-angiopoietin aptamers, whose performances are known. We rank the in silico produced configurations, adopting a maximum likelihood estimate, based on their topological and electrical properties. From the analysis, two principal kinds of conformers are identified, whose ability to mimick the binding features of the natural receptor is discussed. The procedure is easily generalizable to many biological biomolecules, useful for increasing chances of success in designing high-specificity biosensors (aptasensors).