BioExcel runs an innovative training programme that is developed and adapted to the needs of the research community through user surveys and competency profiles. The programme consists of a portfolio of training material which can be accessed through this page and we can also deliver a variety of training events such as workshops, tutorials, hands-on which are tailored to particular user needs. We can also contribute to your event, based on our core domains of expertise.

Whether you are new to our core software (GROMACS, HADDOCK, PMX, BioBB) 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 which you can find below. Our current portfolio of training topics, which are regularly updated based on user training requests, includes a comprehensive lecture focusing on the principles and concepts as well as corresponding hands-on tutorial supported by our core software.

  • There are 4 core modules (Molecular Dynamics simulations, Integrative Modelling, Free Energy calculations, Workflow solutions) to choose from.
  • The training material has been divided into 3 categories: Beginner, Intermediate, Advanced.
  • The duration of the training in each module (lecture + hands-on tutorial) is about 0.5 – 1 day, depending on the number of topics requested.

In addition to the links provided for each code below, you can visit http://docs.bioexcel.eu 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.

Module 1: Molecular Dynamics simulations

Beginner
  • Introduction to Molecular Dynamics simulations
  • Introduction to Membrane-Protein Simulation
Intermediate
  • Free energy calculation and alchemical transformations in GROMACS
  • Efficiently use CPU and GPU resources in GROMACS simulations
  • Umbrella sampling
  • Free energy of solvation
Advanced
  • Enhanced sampling methods and Accelerated Weight Histogram (AWH) method
  • Potential of mean force using AWH method
  • Free energy of solvation using AWH method

Module 2: Integrative Modelling

Beginner
  • HADDOCK2.4 basic protein-protein docking
  • HADDOCK2.4 basic antibody-antigen docking
  • PowerFit usage
  • PowerFit web server
  • DisVis web server
Intermediate
  • HADDOCK2.4 local installation
  • HADDOCK2.4 basic Protein-DNA
  • HADDOCK2.4 MS cross-links
  • HADDOCK2.4 CA-CA restraints guided docking
  • HADDOCK2.4 antibody-antigen docking
  • HADDOCK3 antibody-antigen docking
Advanced
  • 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
  • Integrative modelling of the apo RNA-Polymerase-III complex from MS cross-linking and cryo-EM data

Module 3: Free Energy calculations

Prerequisite knowledge: Module 1 (Beginner)
Beginner
  • Introduction to free energy calculations
  • PMX Webserver
Intermediate
  • Amino acid mutations
  • Ligand modifications

Module 4: Workflow solutions

Prerequisite knowledge: Module 1 (Beginner), Module 2 (Beginner), Module 3 (Beginner)
Beginner
  • Interoperable and reproducible biomolecular simulation workflows using BioBB
  • GROMACS Protein MD Setup
  • Automatic Ligand parameterization
  • GROMACS Protein-Ligand Complex MD Setup
  • 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
Intermediate
  • How to use BioBB workflows in Command-Line-Interface
  • BioBB with Common Workflow Language (CWL)
  • Mutation Free Energy Calculations
Advanced
  • How to run HPC-focused workflows with BioBB and PyCOMPSs