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Updated: Mar 7, 2026

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Published on: January 5, 2017

pmx Webserver: A User Friendly Interface for Alchemistry.

Vytautas Gapsys¹, Bert L de Groot¹

¹Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, Göttingen, 37077, Germany.

Journal of Chemical Information and Modeling

|February 10, 2017

Summary

This summary is machine-generated.

This study introduces a web server for alchemical free energy calculations, simplifying amino acid mutation analysis in molecular dynamics simulations. It provides hybrid protein structures and topologies compatible with Gromacs for enhanced protein stability studies.

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Last Updated: Mar 7, 2026

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Area of Science:

Computational chemistry
Biophysics
Molecular modeling

Background:

Alchemical free energy calculations are increasingly used for molecular dynamics simulations.
Usability of these methods for amino acid mutations can be improved.

Purpose of the Study:

To develop a web-based infrastructure for generating hybrid protein structures and topologies for alchemical free energy calculations.
To facilitate amino acid mutation analysis and protein stability studies.

Main Methods:

Development of a webserver for amino acid mutation selection across five molecular mechanics force fields.
Support for complete mutation scans with user-defined amino acids.
Generation of output files compatible with the Gromacs molecular dynamics engine.

Main Results:

The webserver provides hybrid protein structures and topologies for alchemical free energy calculations.
A database of input files and precalculated free energy differences for tripeptides is available.
Demonstrated utility through an alanine scan and thermodynamic stability investigation of the Trp cage mini protein.

Conclusions:

The developed webserver simplifies and enhances the usability of alchemical methods for studying amino acid mutations.
The infrastructure aids in protein stability investigations and molecular dynamics simulations.
The tool is accessible at http://pmx.mpibpc.mpg.de.