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