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
- SBROD – Smooth 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
- SAMSON
