Generative models of conformational dynamics.
Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term 'generative' refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GRAPHICAL MODELS OF ENERGY LANDSCAPES), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc.) from long timescale simulation data.
Carnegie Mellon University, Pittsburgh, PA, USA, cjl@cs.cmu.edu.
Christopher James
CJ
Langmead
D000494:Allosteric Regulation; D000911:Antibodies, Monoclonal / Q000737:chemistry; D015704:CD4 Antigens / Q000737:chemistry; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D023581:HIV Fusion Inhibitors / Q000737:chemistry; D015497:HIV-1 / Q000737:chemistry; D018398:Homeodomain Proteins / Q000737:chemistry; D006801:Humans; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D016011:Normal Distribution; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding
D000911:Antibodies, Monoclonal; D015704:CD4 Antigens; D015699:HIV Envelope Protein gp120; D023581:HIV Fusion Inhibitors; D018398:Homeodomain Proteins; C481504:ibalizumab