BioExcel runs an innovative training programme that is adapted to the needs of the research communities. The programme is developed based on user surveys and competency profiles through which we identify areas of high interest and need for increase expertise. Our training material and offerings aim to fill the skill gaps of researchers and improve their scientific work.

We can deliver a variety of training events such as workshops, tutorials, hands-on which are tailored to the user needs. We can also contribute to your event, on our core domains of expertise. Below you can find our current portfolio of training topics, which we continuously expand.

Whether you are new to the codes or you already have some experience, we have collated a number of relevant learning and support resources to help you out in your own studies. In addition to the links provided for each code below, you can visit to access a wide range of resources. Moreover, through our Ambassador Program we are organizing bi-annual workshops around Europe. The content of those workshops is tailored to the needs of the user communities in the respective regions.

Molecular Dynamics Simulations

Fast, flexible, Free, GROMACS
  • Introduction to Molecular Dynamics simulations
  • Free energy calculation and alchemical transformation in GROMACS
  • Efficiently use CPU and GPU resources in GROMACS simulations
  • Enhanced sampling methods and Accelerated weight histogram method
  • Introduction to Membrane-Protein Simulation
  • Umbrella sampling
  • Free energy of solvation
  • Potential of mean force using AWH method
  • Free energy of solvation using AWH method

Integrative Modelling

  • HADDOCK2.4 local installation
  • HADDOCK2.4 basic protein-protein docking
  • HADDOCK2.4 basic antibody-antigen docking
  • HADDOCK2.4 basic Protein-DNA
  • HADDOCK2.4 MS cross-links
  • HADDOCK2.4 CA-CA restraints guided docking
  • HADDOCK2.4 antibody-antigen docking
  • HADDOCK2.4 ab-initio, multi-body symmetrical docking
  • HADDOCK2.4 shape-restrained protein-small molecule
  • HADDOCK2.4 ligand binding site
  • DISVIS/HADDOCK2.4 oligomer puzzle
  • LightDock+HADDOCK membrane proteins
  • HADDOCK3 documentation including installation instructions
  • HADDOCK3 antibody-antigen
  • PowerFit usage
  • PowerFit web server
  • DisVis web server
  • Integrative modelling of the apo RNA-Polymerase-III complex from MS cross-linking and cryo-EM data

Free Energy Calculations

  • Introduction to free energy calculations
  • Amino acid mutations
  • Ligand modifications
  • PMX Webserver

Workflow solutions

  • Interoperable and reproducible biomolecular simulation workflows using BioBB
  • How to use BioBB workflows in
  • BioBB with Common Workflow Language
  • How to run HPC-focused workflows with BioBB
    and PyCOMPSs
  • GROMACS Protein MD Setup
  • Automatic Ligand parameterization
  • GROMACS Protein-Ligand Complex MD Setup
  • Mutation Free Energy Calculations
  • Protein-ligand Docking (Cluster90)
  • Protein-ligand Docking (PDBe REST-API)
  • Protein-ligand Docking (fpocket)
  • Molecular Interaction Potentials
  • Protein conformational ensembles generation
  • Macromolecular Coarse-Grained Flexibility
  • Protein conformational transitions calculations
  • AMBER Protein MD Setup
  • AMBER Protein-ligand complex MD Setup
  • AMBER Constant pH MD setup
  • ABC MD Setup
  • Structural DNA helical parameters
  • Molecular Structure Checking