Modeling and Studying Proteins with Molecular Dynamics

摘要: Publisher Summary This chapter describes the modeling and studies of proteins using molecular dynamics. A number protein structure–function questions can be addressed with a dynamics program, such as CHARMM. Simple geometric quantities, distance between two atoms, angle three dihedral four locations holes in protein, or surface area determined. The interaction energies any atoms residues other calculated. potential function used by CHARMM, from which forces needed for trajectory calculations are derived, approximates on an atom sum its pairwise interactions system. It is found that files containing coordinates coordinate trajectories produced CHARMM also often input to display programs.