• Alchemical free energy calculations
  • pmx - Automated protein, DNA and ligand hybrid structure and topology generation for free energy calculations.
    pmx webserver - A web server for an automated amino and nucleic acid hybrid structure/topology generation.

  • (Protein) structure generation from distance constraints
  • Concoord - Conformational sampling algorithm and alternative to MD.
    tConcoord - A Concoord variant specialized at conformational transitions.
    Pymol plugin for tConcoord - A PyMOL plugin for tCONCOORD which allows visualization of interactions and interactive constraint definition.

  • Molecular Docking
  • Pymol autodock plugin. - A PyMOL plugin for Autodock which helps setting up docking runs and view docking results with PyMOL.

  • Functional Mode Analysis
  • FMA - Implementation of PCA-based or PLS-based (new) FMA.

  • Tools for Structure Analysis of Biological Macromolecules
  • g_lomepro - Local Membrane Property Analysis.
    Find the up-to-date version of g_lomepro on github.

    Maptools - A number of programs to deal with experimental (X-ray, EM) 3D maps.

    minVar - Superpositioning of flexible molecule ensembles.