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McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm.

Mirco S Till¹, G Matthias Ullmann

¹Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, Bayreuth, Germany.

Journal of Molecular Modeling

|July 24, 2009

Summary

This study introduces a Monte Carlo method to calculate molecular volume using random point placement. The McVol program efficiently detects cavities and potential water binding sites in molecules like proteins.

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Area of Science:

Computational chemistry
Structural biology
Biophysics

Background:

Accurate molecular volume determination is crucial for understanding molecular interactions and properties.
Identifying internal cavities and surface clefts is essential for predicting molecular function, such as water binding.
Existing methods may lack efficiency or comprehensive cavity detection capabilities.

Purpose of the Study:

To develop and present a novel Monte Carlo method for calculating the volume of molecules.
To implement a computational tool (McVol) for efficient molecular volume and cavity analysis.
To demonstrate the application of this method in identifying potential water binding sites in proteins.

Main Methods:

A Monte Carlo approach using random point distribution within a bounding box to estimate molecular volume.
Modeling molecules as overlapping hard spheres with a surface defined by a rolling probe sphere.
Employing a grid-cell based neighbor list for computational efficiency in point-in-molecule tests.
Utilizing a graph-theoretical algorithm in conjunction with volume calculation to detect internal cavities and surface clefts.

Main Results:

The Monte Carlo method accurately estimates molecular volume by calculating the ratio of internal to total random points.
The McVol program efficiently identifies internal cavities and surface clefts, which are potential sites for water molecule binding.
The method was successfully applied to several proteins, demonstrating its practical utility in structural analysis.

Conclusions:

The developed Monte Carlo method provides an efficient and accurate means for determining molecular volume.
The McVol program offers a valuable tool for researchers in computational chemistry and structural biology for cavity and cleft analysis.
The identification of potential water binding sites through cavity detection has implications for molecular dynamics and other computational studies.