A Discrete Geometry Method for Atom Depth Computation in Complex Molecular Systems

Sara Marziali, Giacomo Nunziati, Alessia Lucia Prete, Neri Niccolai, Sara Brunetti, Monica Bianchini

Abstract: The field of structural biology is rapidly advancing thanks to significant improvements in X-ray crystallography, nuclear magnetic resonance (NMR), cryo-electron microscopy, and bioinformatics. The identification of structural descriptors allows for the correlation of functional properties with characteristics such as accessible molecular surfaces, volumes, and binding sites. Atom depth has been recognized as an additional structural feature that links protein structures to their folding and functional properties. In the case of proteins, the atom depth is typically defined as the distance between the atom and the nearest surface point or nearby water molecule.

External IDs:dblp:conf/dgmm/MarzialiNPNBB24