Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking

Efficient computational techniques provide advantageous solutions for complex problems in molecular modeling and related fields. These computational algorithms can come at hand where “wet biology” cannot be, or is too expensive to be carried out; they also help in solving computational bottlenecks caused when using the direct calculation. Here we illustrate these ideas by presenting two computational methods. The first algorithm provides a linear-complexity multiscale computation of the many-body problem of calculating long-range electrostatics in charge and dipolar systems [1,2]. The second method brings a Computer Vision approach to a biomolecular structural recognition problem, namely, an automated method for molecular docking [3, 4, 5, 6, 7, 8]. We conclude by demonstrating a possible implementation of electrostatic docking, i.e., combining the use of our multiscale fast electrostatics method in molecular docking.