• Calendar

December 30, Tuesday
12:00 – 14:00

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.