Wielding the power of interactive molecular simulations

Abstract

AbstractSince the dawn of the computer age, scientists have designed devices to represent molecular structures and developed tools to simulate their dynamic behavior in silico. To this day, these tools remain central to our understanding of biomolecular phenomena. In contrast to other fields such as fluid mechanics or meteorology, the observation of molecular motions at the atomic level remains a major experimental challenge. Continuous advances in computer graphics and numerical computation, combined with the emergence of human–computer interaction approaches, led to the methodology of so‐called “interactive molecular simulations”, characterized by two main features. First, the possibility to visualize a running simulation in interactive time, that is, compatible with human perception. Second, the possibility to manipulate the simulation interactively by imposing a force, changing a biophysical property, or editing runtime parameters on the fly. Such simulations are still little used in computational biology, where it is more common to run a series of offline simulations and then visualize and analyze the results. However, interactive molecular simulation tools promise to handle time‐consuming tasks such as the modeling of particularly complex biomolecular structures more efficiently or to support approaches such as Rational Drug Design with regard to pharmaceutical applications.This article is categorized under: Computer and Information Science > Computer Algorithms and Programming Computer and Information Science > Visualization Software > Simulation Methods