BioExcel software tools for intermediate to advanced users
Date: 26 - 28 November 2024
Timezone: Lisbon
Duration: 2.5 days
Our second Ambassador Program workshop is jointly organised with and supported by our colleagues at the National Competence Centres in Portugal, France, Spain and Ireland. The hands-on 2.5-day workshop will be a hybrid (on-site/online) event and will focus on the use of BioExcel core codes: GROMACS, HADDOCK, PMX and BioBB; and will include an Alphafold tutorial.
Participation: Open application with a selection. 40 applicants will be selected for on-site participation. Applicants from Portugal, France, Spain and Ireland will be prioritised for on-site participation. We can only accept participants from EuroHPC Joint Undertaking member institutions.
Registration fee: free
Program:
The program is under development and will contain the following elements:
Introduction to GROMACS (membrane-protein simulations) including how to perform alchemical transformation with GROMACS
HADDOCK Antigen-Antibody or/and Protein-DNA modelling
BioBB tutorial on protein conformational transitions calculations and automatic ligand parameterization
Advance free energy method / amino acid mutations
AlphaFold tutorial
Keywords: GROMACS, BioExcel, HADDOCK, PMX, BioBB, Workshop
City: Coimbra
Country: Portugal
Prerequisites:
The participants must have experience in basic Linux/Unix skills. Ability to use the command line: navigate files and directories through shell commands, create/move/delete files and directories, set environment variables etc.
Learning objectives:
- Set up simple and complex (membrane-based) simulation systems and perform alchemical transformations using GROMACS.
- GROMACS deployment on GPU-accelerated HPC systems
- Familiarity with using HADDOCK for protein modelling in complex environments
- Ability to use BioBB workflow
- Perform free-energy calculations for protein systems
Organizer: BioExcel, NCC Portugal, University of Coimbra
Host institutions: University of Coimbra
Capacity: 40
Event types:
- Workshops and courses
Cost basis: Free to all
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