A New Analytical Method for Computing Solvent Accessible Surface Area and its Gradients for Macromolecules

TL;DR

This paper introduces a new analytical algorithm for calculating solvent accessible surface area of macromolecules, transforming the 3D problem into 2D integrals, which improves accuracy and performance.

Contribution

The paper presents a novel analytical method that simplifies the computation of solvent accessible surface area by mapping 3D intersections onto 2D plane integrals, enabling parallelization.

Findings

High accuracy demonstrated on small proteins

Good computational performance

Suitable for parallel processing

Abstract

In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a new analytical method for this purpose. In the proposed algorithm, we consider the transformation which maps the spherical circles of intersection of atomic surfaces in three-dimensional space onto the circles on a two-dimensional plane and the problem of computing solvent accessible surface area is transformed into the problem of computing corresponding curve integrals on the plane. This allows to consider only integrals over the circular trajectories on the plane. The algorithm is suitable for parallelization. Testings on several small proteins have shown a high accuracy of the algorithm and a good performance.