QUANTIFICATION AND VISUALIZATION OF MOLECULAR-SURFACE FLEXIBILITY

Two new methods for the quantification and visualization of the flexib ility of molecular surfaces are presented. Both methods rely on result s of molecular dynamics (MD) simulations. Whereas method I is based on a simple but fast grid-counting algorithm, method II uses a mapping f unction that allows for a sharp and clear visualization of atomic RMS fluctuations on a molecular surface. To demonstrate the scope of the m ethods, MD simulations of two proteins, PTI and ubiquitin, were perfor med. The flexibility data are mapped onto the molecular surfaces of th e proteins and visualized using texture mapping technology available o n modern workstations.