In silico maturation: Processing sequences to improve biopolymer functions based on genetic algorithms

Abstract

Peptide ligands and oligonucleotide aptamers are promising agents in therapeutic and diagnostic applications. Conventional technologies to develop these biopolymers depend on screening of functional sequences from a combinatorial library. Because the relationship between a biopolymer sequence and its function is a complex and multidimensional problem, identification of sequences for a desired function cannot be readily accomplished only by rational approaches. To solve such problems, genetic algorithms (GAs) represent an intelligent strategy to perform random search in a defined sequence space. This methodology permits progressive exploration of the sequence space and evolving biopolymer functions. In this chapter, we present an overview of GA-based approaches to develop functional peptide ligands and oligonucleotide aptamers. We review recent trends in GA-based optimization of biopolymer sequences to improve targeted functions.