title: HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins.
abstract: BACKGROUND
  A large fraction of eukaryotic proteins contain unstructured tails or linkers. The presence of flexible regions allows these systems to experience a high level of mobility facilitating their biological function. The complex nature of protein rotation in such flexible modular systems precludes a straightforward application of hydrodynamic methods to calculate their rotational motional properties. We describe the workflow of HYdrodynamic CoUpling of Domains (HYCUD), a program for prediction of effective rotational correlation times in multidomain proteins. The usage of HYCUD is demonstrated by its application to the ribosomal protein L7/L12. Rotational correlation times predicted by HYCUD might be used to detect molecular switch events mediated by disorder-order transitions in interdomain linkers.
  
  
  METHODS
  The source code and documentation are available at www.mpibpc.mpg.de/106144/software.
  
  
  BACKGROUND
  mzwecks@gwdg.de or nare@nmr.mpibpc.mpg.de
  
  
  BACKGROUND
  Supplementary material is available at Bioinformatics online.
authors.affiliation: Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.
authors.forename: Nasrollah
authors.initials: N
authors.lastname: Rezaei-Ghaleh
authors.affiliation: Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.
authors.forename: Frederik
authors.initials: F
authors.lastname: Klama
authors.affiliation: Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.
authors.forename: Francesca
authors.initials: F
authors.lastname: Munari
authors.affiliation: Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany and Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Zweckstetter
mesh_terms: D019295:Computational Biology / Q000379:methods*; D017434:Protein Structure, Tertiary; D012269:Ribosomal Proteins / Q000737:chemistry*; D012399:Rotation; D012984:Software
chemical_list: D012269:Ribosomal Proteins; C016700:ribosomal protein L7-L12