If you are using this web server, please cite:
Vytautas Gapsys and Bert L. de Groot.
pmx Webserver: A User Friendly Interface for Alchemistry.
J. Chem. Inf. Mod.
DOI: 10.1021/acs.jcim.6b00498 (2017).
Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, and Bert L. de Groot.
pmx: Automated protein structure and topology generation for alchemical perturbations.
J. Comput. Chem.
36:348-354 (2015).
For DNA mutations, please cite:
Vytautas Gapsys and Bert L. de Groot.
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes.
J. Chem. Theory Comput.
DOI: 10.1021/acs.jctc.7b00849 (2017).
For the force field evaluation using pmx cite:
Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot.
Accurate and Rigorous Large Scale Mutation Free Energy Prediction.
Angewandte Chemie Int. Ed.
55: 7364-7368(2016)
Brief Summary.
In this work we compared a number of contemporary molecular dynamics force fields in a large scale mutational scan
probing protein thermodynamic stability.
We have used an enzyme barnase as a test system and calculated double free energy differences for 119 mutations (88 charge conserving and
31 charge changing mutations).
On average the best performing force fields (Amber99sb*ILDN, Charmm22* and Charmm36) achieved a remarkable accuracy with the
average unsigned deviation from the experimental measurements reaching ~1 kcal/mol.
Furthermore, we observed an improvement in the estimation accuracy when combining free energy values from several force fields.
A simple averaging over the calculated free energy values from the Amber99sb*ILDN and one of the Charmm family force fields
allowed obtaining average unsigned error below 1 kcal/mol.
Such a consensus force field approach appeared to hold in other protein systems as well.
AWS benchmark study:
Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L de Groot, Vytautas Gapsys. GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. J. Chem. Inf. Model. in revision (2022)
The study where pmx (pymacs at that time) was introduced:
Daniel Seeliger and Bert L. de Groot.
Protein thermostability calculations using alchemical free energy simulations.
Biophys. J.
98:2309-2316 (2010)