14: Modelling and Simulation of Proteins Check Access

Proteins are biopolymers with a complex structure and flexibility, both of which are intrinsically linked with the important functions that proteins carry out in organisms and in biotechnology applications. The first part of this chapter explains the main template-based and template-free methods of protein structure prediction, namely comparative modelling, threading/fold recognition, ab initio modelling and contact-based modelling. The second part explains the method of molecular dynamics simulation of proteins, which is used to simulate protein flexibility. In addition to standard procedures, basic data analysis and limitations are discussed. Techniques to overcome some of the limitations, such as polarisable force fields and enhanced sampling techniques, are summarised. This chapter enables readers to understand the research literature in this area and to move forward to more practical tutorials and apply the methods themselves.