New open access book chapter: Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations

Molecular simulations allow researchers to obtain complementary data with respect to
experimental studies and to overcome some of their limitations. Current experimental
techniques do not allow to observe the full dynamics of a protein at atomic detail. In
return, experiments provide the structures, i.e. the spatial atomic positions, for numerous
biomolecular systems, which are often used as starting point for simulation studies. In order
to predict, to explain and to understand experimental results, researchers have developed a
variety of biomolecular representations and algorithms. They allow to simulate the dynamic
behavior of macromolecules at different scales, ranging from detailed models using quantum
mechanics or classical molecular mechanics to more approximate representations. These
simulations are often controlled a priori by complex and empirical settings. Most researchers
visualise the result of their simulation once the computation is finished. Such post-simulation
analysis often makes use of specific molecular user interfaces, by reading and visualising the
molecular 3D configuration at each step of the simulation. This approach makes it difficult
to interact with a simulation in progress. When a problem occurs, or when the researcher
does not achieve to observe the predicted behavior, the simulation must be restarted with
other settings or constraints. This can result in the waste of an important number of compute
cycles, as some simulations last for a long time: several days to weeks may be required
to reproduce a short timespan, a few nanoseconds, of molecular reality. Moreover, several
biomolecular processes, like folding or large conformational changes of proteins, occur on
even longer timescales that are inaccessible to current simulation techniques.

A. Tek, B. Laurent, M. Piuzzi, Z. Lu, M. Baaden, O. Delalande, M. Chavent, N. Férey, C. Martin, L. Piccinali, B. Katz, P. Bourdot, Ludovic Autin ;
Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations ; W. Cai and H. Hong ; Intech, Croatia