The NANO-D group develops and supports multiple software tools for molecular modeling and simulations:

  • S-GCN – Spherical convolutions on molecular graphs for protein model quality assessment
  • VoroCNN – Deep convolutional neural network built on 3D Voronoi tessellation of protein structures
  • KORP-PL – a very efficient coarse-grained potential to score protein-ligand complexes
  • NOLB non-linear normal modes – a new conceptually simple and computationally efficient method for non-linear normal mode analysis
  • PEPSI-SAXS – a new implementation of the multipole-based scheme for X-ray small-angle scattering profile calculations
  • PEPSI-SANS – an extension of the Pepsi-SAXS method for small-angle neutron scattering
  • PEPSI-Dock – a protein-protein docking prediction algorithm which uses a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation
  • 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 – a protein-ligand potential
  • OffGridFit – a novel FFT-based exhaustive search method extended to off-grid translational and rotational degrees of freedom
  • AnAnaS – an Analytical Analyser of molecular Symmetries
  • SBRODSmooth Backbone-Reliant Orientation- Dependent scoring function for protein model quality assessment
  • Ornate – Oriented Routed Neural network with Automatic Typing – a 3D CNN method for protein model quality assessment
  • DeepSymmetry – a 3D CNN method for detection of structural repetitions in proteins and their density maps

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