Wolumes - An algorithm to compute the volume of atoms and residues in proteins

TL;DR

Wolumes is a fast, stand-alone C program that accurately measures atom volumes in proteins using a grid-based discretization, aiding in identifying abnormal atomic and residue sizes.

Contribution

It introduces a simple, efficient algorithm for calculating atom volumes in proteins, optimized with van der Waals radii, and provides a freely available source code.

Findings

Accurately measures atom volumes in proteins.

Identifies abnormally large or small atoms and residues.

Provides a validated, open-source tool for structural analysis.

Abstract

Wolumes is a fast and stand-alone computer program written in standard C that allows the measure of atom volumes in proteins. Its algorithm is a simple discretization of the space by means of a grid of points at 0.75 Angstroms from each other and it uses a set of van der Waals radii optimized for protein atoms. By comparing the computed values with distributions derived from a non-redundant subset of the Protein Data Bank, the new methods allows to identify atoms and residues abnormally large/small. The source code is freely available, together with some examples.