Protocol for Simulations of PEGylated Proteins with Martini 3

Fabian Grünewald, Peter C Kroon, Paulo C T Souza, Siewert J Marrink*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review


Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (MD) simulations can be applied to study specific protein-polymer systems at molecular level detail. Here we present instructions on how to simulate PEGylated proteins using the latest iteration of the Martini coarse-grained (CG) force-field. CG MD simulations offer near atomistic information and at the same time allow to study complex biological systems over longer time and length scales than fully atomistic-level simulations.

Original languageEnglish
Title of host publicationStructural Genomics
EditorsY.W. Chen , CP.B. Yiu
Place of PublicationNew York
PublisherHumana Press
Number of pages21
ISBN (Electronic)978-1-0716-0892-0
ISBN (Print)978-1-0716-0891-3
Publication statusPublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Martini
  • Proteins
  • Polymers
  • PEGylation
  • Coarse-grained simulation
  • Modified proteins

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