The NANO-D group develops several software for molecular modeling and simulation:

  • NOLB non-linear normal modes – a new conceptually simple and computationally efficient method for non-linear normal mode analysis
  • PEPSI-Dock – a protein-protein docking prediction algorithm which uses a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation
  • PEPSI-SAXS – a new implementation of the multipole-based scheme for X-ray small-angle scattering profile calculations
  • DockTrina –  a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers
  • HermiteFit –  a new docking algorithm for rapid fitting atomic structures into cryo-EM density maps using 3D orthogonal Hermite functions
  • RigidRMSD –  library for constant-time computations of the root mean square deviations
  • RapidRMSD – library for rapid root mean square deviations, including rigid transformations and flexibility modeled with collective motions
  • Knodle – KNOwledge-Driven Ligand Extractor,  a software library for the recognition of atomic types, their hybridization states and bond orders in the structures of small molecules
  • Convex-PL protein-ligand potential
  • Protein folding potential
  • OffGridFit – a novel FFT-based exhaustive search method extended to off-grid translational and rotational degrees of freedom.

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