title: PyTMs: a useful PyMOL plugin for modeling common post-translational modifications.
abstract: BACKGROUND
  Post-translational modifications (PTMs) constitute a major aspect of protein biology, particularly signaling events. Conversely, several different pathophysiological PTMs are hallmarks of oxidative imbalance or inflammatory states and are strongly associated with pathogenesis of autoimmune diseases or cancers. Accordingly, it is of interest to assess both the biological and structural effects of modification. For the latter, computer-based modeling offers an attractive option. We thus identified the need for easily applicable modeling options for PTMs.
  
  
  RESULTS
  We developed PyTMs, a plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of common PTMs into protein/peptide models and can be used to address research questions related to PTMs. Ten types of modification are currently supported, including acetylation, carbamylation, citrullination, cysteine oxidation, malondialdehyde adducts, methionine oxidation, methylation, nitration, proline hydroxylation and phosphorylation. Furthermore, advanced settings integrate the pre-selection of surface-exposed atoms, define stereochemical alternatives and allow for basic structure optimization of the newly modified residues.
  
  
  CONCLUSIONS
  PyTMs is a useful, user-friendly modelling plugin for PyMOL. Advantages of PyTMs include standardized generation of PTMs, rapid time-to-result and facilitated user control. Although modeling cannot substitute for conventional structure determination it constitutes a convenient tool that allows uncomplicated exploration of potential implications prior to experimental investments and basic explanation of experimental data. PyTMs is freely available as part of the PyMOL script repository project on GitHub and will further evolve. Graphical Abstract PyTMs is a useful PyMOL plugin for modeling common post-translational modifications.
authors.affiliation: Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Applied Immunology & Immunotherapy, L8:04, Karolinska Hospital, SE-171 76, Stockholm, Sweden. andreas.warnecke@ki.se.
authors.forename: Andreas
authors.initials: A
authors.lastname: Warnecke
authors.affiliation: Department of Medicine Solna, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. Tatyana.Sandalova@ki.se.
authors.forename: Tatyana
authors.initials: T
authors.lastname: Sandalova
authors.affiliation: Department of Medicine Solna, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. Adnane.Achour@ki.se.
authors.forename: Adnane
authors.initials: A
authors.lastname: Achour
authors.affiliation: Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Applied Immunology & Immunotherapy, L8:04, Karolinska Hospital, SE-171 76, Stockholm, Sweden. robert.harris@ki.se.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Harris
mesh_terms: D000818:Animals; D002417:Cattle; D051638:Ether-A-Go-Go Potassium Channels / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012710:Serum Albumin, Bovine / Q000737:chemistry / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D051638:Ether-A-Go-Go Potassium Channels; C496884:KCNH1 protein, human; D010446:Peptide Fragments; D011506:Proteins; D012710:Serum Albumin, Bovine