Docking
  • PatchDock - molecular docking algorithm based on shape complementarity principles
  • PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.
  • SymmDock - prediction of complexes with Cn symmetry by geometry based docking
  • SymmDock is an algorithm for prediction of complexes with Cn symmetry by geometry based docking. Given the structure of the asymmetric unit of the multimer complex, SymmDock predicts the structure of the entire complex. A Cn symmetry type complex is a complex with a rotational symmetry of order n about a symmetry axis. The rotation angle alpha is of 360/n degrees.
    Modeling with SAXS profiles
  • FoXS - fast SAXS profile computation with Debye formula
  • SAXS experiment determines 1-dimensional structural information, termed SAXS profile, which is the scattering intensity of a molecule as a function of spatial frequency. FoXS is a method for computing a theoretical scattering profile of a structure and fitting of experimental profile.
  • MultiFoXS - multi-state modeling with SAXS profiles
  • MultiFoXS is a method for multi-state modeling with SAXS profiles. The method was developed for interpretation of data collected for heterogeneous samples. Many proteins are conformationally heterogeneous in solution. We describe this heterogeneity using multi-state models. A multi-state model is a model that specifies two or more co-existing structural states and values for any other parameter, such as population weights.
  • FoXSDock - macromolecular docking with SAXS Profile
  • FoXSDock is a method for docking with SAXS profile of the complex. The input is two proteins and a SAXS profile of their complex. The output is a list of potential complexes sorted by a score that combines interface energy and the fit to SAXS profile.
  • SAXS tutorial files - input files for FoXS, MultiFoXS, BilboMD, and FoXSDock.