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.
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)