title: pmx: Automated protein structure and topology generation for alchemical perturbations.
abstract: Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36.
authors.affiliation: Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany.
authors.forename: Vytautas
authors.initials: V
authors.lastname: Gapsys
authors.forename: Servaas
authors.initials: S
authors.lastname: Michielssens
authors.forename: Daniel
authors.initials: D
authors.lastname: Seeliger
authors.forename: Bert L
authors.initials: BL
authors.lastname: de Groot
mesh_terms: D000596:Amino Acids / Q000235:genetics; D001331:Automation; D019295:Computational Biology; D015723:Gene Library; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics; D011487:Protein Conformation; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012984:Software; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: alchemy; free energy calculations; molecular dynamics; mutations; thermostability