AlphaMol 1.0 – Tools for Biomolecular Geometry

AlphaMol 1.0


AlphaMol provides easy to use tools to characterize the geometry of biomolecules.This project provides a collection of tools for computing geometric measures of biomolecules such as volumes and surfaces areas and for identifying their internal cavities and pockets, if any, and computing their measures. By focusing on the geometry of biomolecules, AlphaMol provides means to understand the role of shape in biomolecular functions and dynamics.

AlphaBall contains a suite of program for computing the surface area and volume of unions of balls. It works on millions of balls.

ParsePDB is a simple PDB parser that reads in a PDB file and outputs a generic coordinate files that can be read by geometric packages.


 AlphaMol Team





  • Windows / MacOsX /  Linux





H. Edelsbrunner and P. Koehl.
The geometry of biomolecular solvation.
Combinatorial and Computational Geometry (MSRI Publications), 52, 243-275. (2005)

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