  The need to understand the assembly kinetics of fibril formation has become
urgent because of the realization that soluble oligomers of amyloidogenic
peptides may be even more neurotoxic than the end product, namely, the amyloid
fibrils. In order to fully understand the routes to fibril formation one has to
characterize the major species in the assembly pathways. The characterization
of the energetics and dynamics of oligomers (dimers, trimers etc) is difficult
using experiments alone because they undergo large conformational fluctuations.
In this context, carefully planned molecular dynamics simulation studies,
computations using coarse-grained models, and bioinformatic analysis have given
considerable insights into the early events in the route to fibril formation.
Here, we describe progress along this direction using examples taken largely
from our own work. In this chapter, we focus on aspects of protein aggregation
using Abeta-peptides and prion proteins as examples.
