Computational predictive approaches for interaction and structure of aptamers.

• The computational prediction of aptamer interactions can be useful to provide guidelines for effective aptamer selection and designing with high affinity. • The computational structure prediction can be helpful to improve the selection to have a wider sort of structures and prepares necessary information to simulate molecular docking. • The structure prediction is performed through either sequence-based prediction or structure-based prediction. • Secondary structure prediction methods can be divided into two general categories: single-sequence analysis and multiple sequence analysis. • 3D structure prediction is achieved through template-based and free modeling-based methods. Aptamers are short single-strand sequences that can bind to their specific targets with high affinity and specificity. Usually, aptamers are selected experimentally via systematic evolution of ligands by exponential enrichment (SELEX), an evolutionary process that consists of multiple cycles of selection and amplification. The SELEX process is expensive, time-consuming, and its success rates are relatively low. To overcome these difficulties, in recent years, several computational techniques have been developed in aptamer sciences that bring together different disciplines and branches of technologies. In this paper, a complementary review on computational predictive approaches of the aptamer has been organized. Generally, the computational prediction approaches of aptamer have been proposed to carry out in two main categories: interaction-based prediction and structure-based predictions. Furthermore, the available software packages and toolkits in this scope were reviewed. The aim of describing computational methods and tools in aptamer science is that aptamer scientists might take advantage of these computational techniques to develop more accurate and more sensitive aptamers. [ABSTRACT FROM AUTHOR]