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Use cases

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brindakv edited this page Apr 20, 2017 · 5 revisions

Sali Lab (Integrative Modeling Platform, IMP):

  • Nup84: use of chemical crosslinks and 2DEM data; system represented at multiple levels of resolution (one residue per bead for structured regions, many residues per bead for disordered regions). Bayesian scoring used for crosslinks.
  • SEA complex: chemical crosslinks with ambiguity (stoichiometry of the complex not known experimentally, but likely contains multiple copies of at least some subunits)
  • IMP Tutorial: use of chemical crosslink data in combination with fit to a 3D cryoEM map
  • PhoQ: modeling in multiple states (open/closed form)

Schwede Lab (ModelArchive, MA; SwissModel, SMNG; OpenStructure, OST):

  • Modeling of homomers, heteromers with ligands (in protein - protein interfaces)
  • Models based on evolutionary constraints (Sergey Ovchinnikov, Baker group)
  • de novo models

DiMaio Lab (Rosetta):

  • homology modelling + symmetric docking guided by low-resolution EM (four low-energy clusters consistent with the data; biochemical knowledge was used to determine the correct one)
  • symmetric fold-and-dock guided by NMR restraints + low-resolution density
  • many cases of de novo structure determination and homology model refinement guided by moderate-resolution EM (both symmetric and non symmetric)
  • domain docking and assembly in low-resolution EM

Hummer Lab (COMPLEXES, EROS)

  • ATG1-complex: Tetramer of tetramers (Atg17-Atg31-Atg29-Atg1-Atg13), 4448 residues. Missing residues and loops modeled as flexible linkers (3 rigid domains, 52 linkers). EROS refined coarse-grained simulations (COMPLEXES, 1AA =1bead) using SAXS data. Ensemble of ~100 dynamic structures.
  • ESCRT-I-II supercomplex: multi-subunit protein complex. Stoichiometry is known and crystal structures exist for the large rigid domains. Experimental conformation data exist from both smFRET and EPR on the same complex. Flexible linkers and rigid domains are modeled with a coarse grained MC simulation approach (1AA = 1bead), in silico smFRET and EPR experiments are performed and evaluated against the experimental data.

Other (deposited elsewhere)

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