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Tools for Molecular Simulation of Neuronal Signaling Cascades - Agenda

Wednesday, 21 June 2023
CEST: 13:00
UTC: 11:00
Second HBPMolSim Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades

2nd Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades

The human brain is one of the most complex and fascinating structures. It is still far from understood and therefore considered one the last biological frontiers. Its function is the result of intricate signal transmission networks and reactions occurring within and between neurons. To model and simulate such complexity, multiscale models are required that are aimed at reproducing brain function through a bottom-up approach, from the molecular to the whole brain level. This workshop will provide training in some of the computational tools developed in the Human Brain Project that enable brain simulation and modelling at the molecular and subcellular levels. This workshop is intended to offer an overview of these tools and their application and provide students and young researchers with the necessary theoretical background and practical experience to enable them to apply them in their own research. There will be a mix of lectures and practical session as well as discussions of case studies and the participants' own research problems.

This workshop is part of the EBRAINS RI trainings. Registration to the training is now open.

Venue for the Hybrid Event

  • on site: Mathematikon, 3rd Floor computer pool, Im Neuenheimer Feld 205, Heidelberg, Germany
  • online: zoom

Registration

For registration to the event a (free of charge) EBRAINS account is required (get it here, if you do not yet have an account): register for the workshop

Registration deadline: 23.05.2023

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CEST: 13:00
UTC: 11:00
Session 1: OMICs and Subcellular Modeling
CEST: 13:00‑13:30
UTC: 11:00‑11:30
(30 min)
 Welcome & introduction

Introduction and overview of the HBP and EBRAINS.

Rebecca Wade (HITS gGmbH)
CEST: 13:30‑14:30
UTC: 11:30‑12:30
(60 min)
 Lecture and Hands-on

Synaptic Proteome Database (Overview and Demo)

Douglas Armstrong (UEDIN, UK), Oksana Sorokina (UEDIN, UK)
CEST: 14:30‑15:00
UTC: 12:30‑13:00
(30 min)
 Break
CEST: 15:00‑16:00
UTC: 13:00‑14:00
(60 min)
 Lecture and Hands-on:

Subcellular toolset

Olivia Eriksson (KTH, Sweden) & Federica Milinanni (KTH, Sweden)
CEST: 16:00‑17:30
UTC: 14:00‑15:30
(90 min)
 Lecture and Hands-on:

Subcellular App

Andrey Stepaniuk (EPFL, Switzerland)
CEST: 17:30‑18:00
UTC: 15:30‑16:00
(30 min)
 Case studies discussionAll tutors

Thursday, 22 June 2023
CEST: 13:00
UTC: 11:00
2nd HBPMolSim Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades, day II
CEST: 13:00
UTC: 11:00
Session 2: Molecular data and molecular dynamics simulations
CEST: 13:00‑14:30
UTC: 11:00‑12:30
(90 min)
 Lecture and hands-on:

CNS ligands/MoDel/Setting up/running molecular dynamics simulations

Adam Hospital (IRB, Spain)
CEST: 14:30‑14:45
UTC: 12:30‑12:45
(15 min)
 Break
CEST: 14:45‑15:15
UTC: 12:45‑13:15
(30 min)
 Lecture:

tauRAMD calculations of protein-ligand dissociation rates

Giulia D’Arrigo (HITS, Germany)
CEST: 15:15‑16:45
UTC: 13:15‑14:45
(90 min)
 Hands-on:

tauRAMD calculations of protein-ligand dissociation rates

Giulia D’Arrigo (HITS, Germany)
CEST: 16:45‑17:00
UTC: 14:45‑15:00
(15 min)
 Break
CEST: 17:00‑18:30
UTC: 15:00‑16:30
(90 min)
 Lecture and Hands-on:

SSB toolkit: from molecular structure to subcellular networks

Alejandro Giorgetti (University of Verona, Italy) and Rui Ribeiro (FZJ, Germany)

Friday, 23 June 2023
CEST: 09:00
UTC: 07:00
2nd HBPMolSim Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades - day III
CEST: 09:00
UTC: 07:00
Session 3: Further molecular simulation techniques (Brownian dynamics and QM/MM)
CEST: 09:00‑11:00
UTC: 07:00‑09:00
(120 min)
 Lecture and Hands-on:

QM/MM interface to compute protein-ligand binding kinetics

Davide Mandelli (FZJ, Germany), Emiliano Ippoliti (FZJ, Germany)
CEST: 11:00‑11:15
UTC: 09:00‑09:15
(15 min)
 Break
CEST: 11:15‑13:15
UTC: 09:15‑11:15
(120 min)
 Lecture and Hands-on:

Brownian dynamics simulations with SDA to compute association rates

Abraham Muniz Chicharro (HITS, Germany), Stefan Richter (HITS, Germany) & Rebecca Wade (HITS, Germany)
CEST: 13:15‑13:45
UTC: 11:15‑11:45
(30 min)
 Lunch Break
CEST: 13:45
UTC: 11:45
Session 4: Molecular Data
CEST: 13:45‑14:30
UTC: 11:45‑12:30
(45 min)
 Lecture:

ACRALL (Nicotinic Acetylcholine Receptor Allosteric Ligand Library

Jean-Pierre Changeux (IP, France), Marco Cecchini (UNISTRA, France)
CEST: 14:30‑15:00
UTC: 12:30‑13:00
(30 min)
 Case studies discussionAll tutors
CEST: 15:00‑15:15
UTC: 13:00‑13:15
(15 min)
 Break
CEST: 15:15
UTC: 13:15
HBP BRAVE Partner project - Open Workshop

The BRAVE project addresses the problem of COVID-19's impact on the brain by tackling COVID-19 brain inflammation by computer-aided molecular design.

The aim of the project is to block SARS-CoV-2 mediated neurodegeneration and brain damage by inhibiting the activation of the NLRP3 inflammasome, which is responsible for neuroinflammation in several neurodegenerative conditions such as Alzheimer's disease and long COVID-19. The results of this project will be presented and discussed in this workshop.

CEST: 15:15
UTC: 13:15
Session 1: Presentations of project achievements
CEST: 15:15‑16:15
UTC: 13:15‑14:15
(60 min)
 Lecture:

Project Introduction and Results, part 1: COVID-19 and neuroinflammation. Identification of new molecules to target neuroinflammation and neurodegeneration.

Francesca Spyrakis (Turin, Italy)
CEST: 16:15‑17:15
UTC: 14:15‑15:15
(60 min)
 Lecture:

Project Results, part 2: NLRP3 monomer Functional Dynamics: from the Effects of Allosteric Binding to Implications for Drug Design

Giorgio Colombo (Pavia, Italy)