Current approaches to flexible loop modeling

Abstract

Loops are key components of protein structures, involved in many biological functions. Due to their conformational variability, the structural investigation of loops is a difficult topic, requiring a combination of experimental and computational methods. This paper provides a brief overview of current computational approaches to flexible loop modeling, and presents the main ingredients of the most standard protocols. Despite great progress in recent years, accurately modeling the conformational variability of long flexible loops remains a challenging problem. Future advances in this field will likely come from a tight coupling of experimental and computational techniques, which would enable a better understanding of the relationships between loop sequence, structural flexibility, and functional roles. In fine, accurate loop modeling will open the road to loop design problems of interest for applications in biomedicine and biotechnology.

Keywords

• Loop modeling
• Protein flexibility
• Conformational sampling
• Structure prediction
• Energy landscapes