Remote BioExcel Winter School on Biomolecular Simulations

Michelle Mendonca
A laptop, cup,notepad and phone on a brown table

After the success of the 2020 Remote Summer School, BioExcel is organising a winter edition of the course.

Date: Monday 30 November – Friday 4 December 2020
Venue: Remote
Application deadline: 18 October 2020
Notification date: 28 October 2020
Participation: Open application with selection
Registration fee: 50 Euros (to be paid after the selection process)
Contact: Michelle Mendonca

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.

– Applications are now closed –

The winter 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)
During the hands-on computer practicals you will make use of the BioExcel flagship software and tools: e.g. GROMACS, HADDOCK, PMX, BioBB. The trainers, developers and/or experts in the use of the software, will provide guidance and support. Audience and Prerequisites The winter 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 18 October. Incomplete applications will not be considered. All applicants will be informed of the status of their application (successful, waiting list, rejected) by 28 October. If you have any questions regarding the application process, please contact Michelle Mendonca (mmendonca@ebi.ac.uk) Tips for a good application 1) During the selection process we focus on:
  • You have the pre-requisite knowledge
  • Your research and your research group will 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. 3) If there are circumstances that make a virtual course especially suitable for you (e.g. travel and financial restrictions, caring responsibilities), please mention this in the application submission section. We highly encourage applications from women and underrepresented groups.
 
Time (CET) Topic Format Trainer
Day 1 - Monday 30 November 
09:00 - 09:20  Course introduction Live Marta Lloret Llinares, Alexandre Bonvin
09:20 - 09:40 BioExcel introduction Live Rossen Apostolov
09:40 - 10:20 Participant presentations Live
10:20 - 10:50 Virtual coffee & tea break
10:50 - 11:40 Docking basics  Pre-recorded lecture 1 Alexandre Bonvin
11:40 - 12:30 Docking basics  Pre-recorded lecture 2 Alexandre Bonvin
12:30 - 12:55 Q&A Live Alexandre Bonvin
12:55 - 14:00 Break
14:00 - 14:40 Participant presentations Live
14:50 - 16:50 Tutorial - HADDOCK Work on your own with live support Alexandre Bonvin, Zuzana Jandova
Time (CET) Topic Format Trainer
Day 2 - Tuesday 1 December 
09:00 - 09:30 Basis of molecular dynamics simulations Pre-recorded lecture 1 Alessandra Villa
09:30 - 10:05 Basis of molecular dynamics simulations Pre-recorded lecture 2 Alessandra Villa
10:05 - 10:30 Q&A Live Alessandra Villa
10:30 - 11:00 Virtual coffee & tea break
11:00 - 12:30 Tutorial - A guide to perform MD simulation with GROMACS Live Christian Blau, Alessandra Villa & Artem Zhmorov
12:30 - 13:30 Break
13:30 - 14:20 BioExcel building blocks (BioBB) Pre-recorded lecture Adam Hospital
14:20 - 15:00 Computational biomolecular simulation workflows using BioBB  Pre-recorded lecture Adam Hospital
15:00 - 15:25 Q&A Live Adam Hospital
15:30 - 16:30 Course social event
Time (CET) Topic Format Trainer
Day 3 - Wednesday 2 December 
09:00 - 09:30 Introduction to QM/MM Pre-recorded lecture 1 Emiliano Ippoliti
09:30 - 10:10 Introduction to QM/MM Pre-recorded lecture 2 Emiliano Ippoliti
10:10 - 10:35 Q&A Live Emiliano Ippoliti
10:40 - 11:10 Virtual coffee & tea break
11:10 - 12:40 Tutorial - Introduction to QM/MM simulations: GROMACS-CP2K Interface Live Dmitry Morozov Vaibhav Modi
12:40 - 13:40 Break
13:40 - 15:10 Tutorial - Protein-Complex MD Setup with Jupyter Notebooks and BioBB Live Adam Hospital
15:15 - 17:00 Poster session
Time (CET) Topic Format Trainer
Day 4 - Thursday 3 December 
09:00 - 10:00 Modeling molecular recognition through enhanced-sampling methods  Pre-recorded lecture 1 Attilio Vargiu
10:00 - 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 - 14:50 Cryo-EM densities vs. Stereochemistry Christian Blau
14:50 - 15:10 Q&A Live
15:10 - 16:10 Round table about career options Rosa M. Badia, Piraveen Gopalasingam, Richard Norman
16:10 - 17:00 Poster and Networking session
Time (CEST) Topic Format Trainer
Day 5 - Friday 4 December 
09:00 - 09:50 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 When HADDOCK meets GROMACS Zuzana Jandova
14:50 - 15:10 Q&A Live
15:10 - 15:30 Using GROMACS and pmx with the BioExcel Building Blocks (BioBB) library to tackle COVID-19 research Adam Hospital
15:30 - 15:50 Q&A Live
15:50 - 16:20 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

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
30 Nov, 2020 - 04 Dec, 2020
10:00 - 18:00

Categories