BioExcel Summer School on Biomolecular Simulations

Beach in cagliari with blue water and orange hues in skies

Date: 4 June (Introduction) and 7 – 11 June 2021
Venue: Remote
Application deadline: 11 April
Notification date: 27 April 
Participation: Open application with selection
Registration fee: 50 Euros (to be paid after the selection process)
Contact: Michelle Mendonca

We highly encourage applications from women and underrepresented groups.

We recognise that participants may occasionally be unable to meet their financial obligations to us for registration fees. If you have been selected for the course and are experiencing financial hardship, problems with obtaining funding, or unsure about how you will pay for fees please talk to us. You can contact Michelle Mendonca at mmendonca@ebi.ac.uk.

– Registrations are now closed – 

The summer school will include lectures and hands-on sessions on the following topics:
  • Molecular Dynamics simulations
  • Biomolecular Docking
  • Free energy calculations
  • Advanced sampling methods (Metadynamics)
  • BioExcel Building Blocks (BioBB)
  • Quantum mechanics/molecular mechanics (QM/MM)
During the hands-on computer practicals you will make use of the BioExcel flagship software and tools: e.g. GROMACS, HADDOCK, PMX, BioBB, and CP2K. The trainers, developers and/or experts in the use of the software, will provide guidance and support.

Audience and Prerequisites

The summer school is intended for researchers (primarily PhD and post-docs) using or planning to use biomolecular modeling and simulation in their everyday research. Familiarity with Linux and basic knowledge of molecular modelling software is a requirement.

To apply you will need the following documents (in word or pdf format):
  • Support letter from your supervisor or a senior co-worker explaining why you should be selected for this course
  • Research Abstract (limit: 250 words – you will be able to present and discuss your research during the course)

Once you have these ready, please complete the application process by midnight (BST) on Sunday 11 April. Incomplete applications will not be considered. All applicants will be informed of the status of their application (successful, waiting list, rejected) by Tuesday 27 April. If you have any questions regarding the application process, please contact Michelle Mendonca.

Tips for a good application

1) During the selection process we focus on:

  • Do you have the pre-requisite knowledge?
  • Will your research and research group benefit from what you learn in this course?
So, please pay special attention to the following 3 questions on the application form:
  • Describe your research interests
  • Describe how this course will benefit your own research
  • Describe how this course will benefit the research of your group
2) You are asked to attach an abstract about the research that you are carrying out and that you will present during the winter school. If you do not have any results yet, you can write your abstract as a short introduction to the topic and a working plan.

This course is designed to ensure full-time participation with flexibility for time zones differences and childcare requirements. This can be discussed with the course coordinator prior to the course to formalise alternative arrangements. We are also organising a career session on Day 4 of the course featuring talks and networking opportunities with professionals from academia and industry.

Note: The programme is subject to minor changes
Time (CEST) Topic Format Trainer
Introduction - Friday 4 June
13:00 - 13:20  Course introduction Live Marta Lloret Llinares and Alexandre Bonvin
13:20 - 13:40  BioExcel introduction Live Rossen Apostolov
13:40 - 15:30 Participant presentations (in blocks of 20 mins with breaks of 10 mins in between) Live  
Time (CEST) Topic Format Trainer
Day 1 - Monday 7 June
09:00 - 09:40 Docking basics  Pre-recorded lecture 1 Alexandre Bonvin
09:50 - 10:30 Docking basics  Pre-recorded lecture 2 Alexandre Bonvin
10:30 - 10:55 Q&A Live Alexandre Bonvin
11:00 - 11:30 Virtual Coffee and Tea Break
11:30 - 13:30 Tutorial - HADDOCK  Live support Alexandre Bonvin, Charlotte van Noort
13:30 - 14:30 Break    
14:30 - 15:10 BioExcel building blocks (BioBB) Pre-recorded lecture Adam Hospital
15:20 - 16:00 Computational biomolecular simulation workflows using BioBB  Pre-recorded lecture Adam Hospital
16:10 - 17:00 Course social event    
Time (CEST) Topic Format Trainer
Day 2 - Tuesday 8 June
09:00 - 09:40 Basis of molecular dynamics simulations Pre-recorded lecture 1 Alessandra Villa
09:50 - 10:30 Basis of molecular dynamics simulations Pre-recorded lecture 2 Alessandra Villa
10:30 - 10:55 Q&A Live Alessandra Villa
11:00 - 11:30 Virtual coffee & tea break
11:30 - 13:00 Tutorial - A guide to perform MD simulation with GROMACS Live Alessandra Villa, Paul Bauer & Berk Hess
13:00 - 14:00 Break
14:00 - 16:00 Tutorial - Protein-Complex MD Setup with Jupyter Notebooks and BioBB, Includes Q&A for BioBB lectures Live Adam Hospital
Time (CEST) Topic Format Trainer
Day 3 - Wednesday 9 June
09:00 - 09:40 Introduction to QM/MM Pre-recorded lecture 1 Emiliano Ippoliti
09:50 - 10:30 Introduction to QM/MM Pre-recorded lecture 2 Emiliano Ippoliti
10:30 - 10:55 Q&A Live Emiliano Ippoliti
11:00 - 11:30 Virtual coffee & tea break
11:30 - 13:30 Tutorial - Introduction to QM/MM simulations Live Dmitry Morozov
13:30 - 14:30 Break
14:30 - 14:50 Constant pH Molecular Dynamics in GROMACS Pre-recorded lecture Noora Aho
14:50 - 15:10 Q&A Live
15:20 - 17:00 Poster session  
Time (CEST) Topic Format Trainer
Day 4 - Thursday 10 June
09:00 - 09:40 Modeling molecular recognition through enhanced-sampling methods  Pre-recorded lecture 1 Attilio Vargiu
09:50 - 10:30 Modeling molecular recognition through enhanced-sampling methods Pre-recorded lecture 2 Attilio Vargiu
10:30 - 10:55 Q&A Live Attilio Vargiu, Giuliano Malloci & Andrea Basciu
11:00 - 11:30 Virtual coffee & tea break
11:30 - 13:30 Metadynamics tutorial - Guided introduction Work on your own with live support Andrea Basciu, Giuliano Malloci & Attilio Vargiu
13:30 - 14:30 Break
14:30 - 15:30 Round table about career options Live Ian Harrow, Holly Judge, Vera Matser, Julien Sindt
15:40 - 17:00 Poster & networking session Live
Time (CEST) Topic Format Trainer
Day 5 - Friday 11 June
09:00 - 09:40 Introduction to free energy calculations  Pre-recorded lecture  Bert de Groot
09:50 - 10:30 Applications of alchemical free energy calculations Pre-recorded lecture  Vytautas Gapsys
10:30 - 10:55 Q&A Live Bert de Groot & Vytautas Gapsys
11:00 - 11:30 Virtual coffee & tea break
11:30 - 13:30 Tutorial - PMX Live Bert de Groot & Vytautas Gapsys
13:30 - 14:30 Break
14:30 - 14:50 MD meets Docking: a use case on antibody design Pre-recorded lecture Alessandra Villa
14:50 - 15:10 Accelerating sampling in GROMACS with the AWH method Pre-recorded lecture Berk Hess
15:10 - 15:40 Q&A
15:45 - 16:10 Final questions, remarks and feedback Live

The lectures and hands-on sessions will be given by internationally recognised leaders in the field of computational biomolecular research.

Speakers

  • Alexandre Bonvin, BioExcel (University of Utrecht)
  • Alessandra Villa, BioExcel (KTH)
  • Christian Blau, BioExcel (KTH)
  • Adam Hospital, BioExcel (IRB Barcelona)
  • Emiliano Ippoliti, BioExcel (FZ Jülich)
  • Bert de Groot, BioExcel (Max Planck Institute)
  • Vytautas Gapsys, BioExcel (Max Planck Institute)
  • Giuliano Malloci, University of Cagliari
  • Attilio Vittorio Vargiu, University of Cagliari
  • Andrea Basciu, University of Cagliari
Organisers
  • Vera Matser, BioExcel (EMBL-EBI)
  • Marta Lloret Llinares, BioExcel (EMBL-EBI)
  • Alexandre Bonvin, BioExcel (University of Utrecht)
  • Attilio Vittorio Vargiu, University of Cagliari
  • Giuliano Malloci, University of Cagliari


Date/Time
04 Jun, 2021 - 11 Jun, 2021
10:00 - 18:00

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