Modeling large macromolecular structures using promolecular densities.
A procedure to easily construct fitted density functions is presented. This methodology, based on the promolecule approach, is able to handle large macromolecular systems, such as proteins. The usual procedure dealing with fitted densities has been improved by adding some restrictions, which allow faster calculations. As a main application example, molecular isodensity contours (MIDCOs) are constructed for two proteins, one of them composed of more than 50 000 atoms. MIDCOs, as a visual representation of the molecular density function, and thus an important descriptor of the molecular charge distribution, constitute a powerful tool in the understanding of molecular systems. MIDCOs are presented for both proteins, allowing exploration of their surfaces, as well as analysis of their shapes. Also, as a quantum mechanical calculation example, molecular quantum self-similarity measures are calculated for several proteins.
Gironés
Xavier
X
Institute of Computational Chemistry, University of Girona, Campus Montilivi, 17071, Girona, Catalonia, Spain.
Amat
Lluís
L
Carbó-Dorca
Ramon
R
D003198:Computer Simulation; D046911:Macromolecular Substances; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry; D011789:Quantum Theory; D055672:Static Electricity
D046911:Macromolecular Substances; D011506:Proteins