Abstract:

Proteins are biological molecules which are involved in virtually every 
process and aspect in life - from the flexing of our muscles to our immune 
system response. It is widely accepted that proteins are dynamic molecules 
with well-defined three-dimensional structures and that understanding the 
structure and dynamics of proteins is crucial for understanding their 
function and the processes they mediate. Various computational methods 
exist for modeling and simulating protein structure and dynamics, but 
several traditional methods are limited due to the large amount of 
calculations involved. This talk will present a wide spectrum of methods 
for searching the conformational space of proteins and their application 
to specific cases. On the one end of the spectrum, Molecular Dynamics 
calculations are used for detailed analysis. On the other end, 
robotics-inspired search techniques are used to characterize the structure 
and dynamics of proteins by representing them using a 
mechanistic/geometric models subject to physics constraints. Two novel 
search methods will be discussed, aimed to characerize the structure, 
dynamics and flexibility of protein structures at various levels of 
details: the first is a hybrid method that combines an efficient 
robotics-inspired sampling algorithm with small scale, detailed 
simulations to characterize the local dynamics of proteins. The second is 
a fast, approximate search method that samples large scale structural 
changes in proteins.