  While many good textbooks are available on Protein Structure, Molecular
Simulations, Thermodynamics and Bioinformatics methods in general, there is no
good introductory level book for the field of Structural Bioinformatics. This
book aims to give an introduction into Structural Bioinformatics, which is
where the previous topics meet to explore three dimensional protein structures
through computational analysis. We provide an overview of existing
computational techniques, to validate, simulate, predict and analyse protein
structures. More importantly, it will aim to provide practical knowledge about
how and when to use such techniques. We will consider proteins from three major
vantage points: Protein structure quantification, Protein structure prediction,
and Protein simulation & dynamics.
  In this chapter we explore basic physical and chemical concepts required to
understand protein folding. We introduce major (de)stabilising factors of
folded protein structures such as the hydrophobic effect and backbone entropy.
In addition, we consider different states along the folding pathway, as well as
natively disordered proteins and aggregated protein states. In this chapter, an
intuitive understanding is provided about the protein folding process, to
prepare for the next chapter on the thermodynamics of protein folding. In
particular, it is emphasized that protein folding is a stochastic process and
that proteins unfold and refold in a dynamic equilibrium. The effect of
temperature on the stability of the folded and unfolded states is also
explained.
