All recordings of the training is published on NCC Türkiye YouTube channel.
Organisation: BioExcel, NCC Sweden, and NCC Türkiye in the context of CASTIEL 2 "Training Sprint" Initiative
Date: April 9-10, 2025
Registration Deadline: 24 March 2025
Event Type: Training
Format: Hybrid (on-site & online)
Skill Level: Intermediate
Language: English
Prerequisites:
-Experience in a Linux environment, jupyter notebook, Python, Conda, and BioBB library.
-Familiarity with High-Performance Computing (HPC) systems is required for participation in the hands-on sessions.
-The training is primarily designed for participants from academia (with at least a graduate degree), industry, or public administration who are using or planning to use biomolecular modeling and simulation in their research.
-Only participants who live and work in the European Union or a country associated with Horizon 2020 are eligible to attend. In line with EuroCC 2 regulations, only official email addresses are accepted for registration; personal or generic emails are not permitted.
For the event programme see the timetable section.
The training consists of four sessions:
1-) Integrative modeling of biomolecular complexes with HADDOCK
Tools, libraries, and applications used:
HADDOCK3: https://github.com/haddocking/haddock3
HADDOCK web server: https://wenmr.science.uu.nl
HADDOCK tutorials: https://bonvinlab.org/education
Learning outcomes:
Getting insights into the field of integrative modeling and more specifically into HADDOCK.
Gaining hands-on experience in the modeling of biomolecular complexes with HADDOCK
Instructor: Alexandre M.J.J Bonvin
About the instructor: Alexandre Bonvin (1964) studied Chemistry at Lausanne University, Switzerland and obtained his PhD at Utrecht University in the Netherlands (1993). After two post-doc periods at Yale University (USA) and the ETHZ (CH) he joined Utrecht University in 1998 where he was appointed full professor of computational structural biology in 2009. In 2006, he received a prestigious VICI grant from the Dutch Research Council. He was director of chemical education (2009-2012), vice head of the Chemistry Department (2010-2012) and Scientific Director of the Bijvoet Centre for Biomolecular Research (2019-2023). He has and is participating to several EU projects including the BioExcel Center of Excellence in Biomolecular Simulations. His work has resulted in over 275 peer-reviewed publications.
Research within his group focuses on the development of reliable bioinformatics and computational approaches to predict, model and dissect biomolecular interactions at atomic level. For this, bioinformatics data, structural information and available biochemical or biophysical experimental data are combined to drive the modelling process. This is implemented and further developed in the widely used HADDOCK software for the modelling of biomolecular complexes (http://bonvinlab.org/software).
2-) Molecular Dynamics Simulations – GROMACS
Tools, libraries, and applications used:
GROMACS: https://www.gromacs.org/
VMD: https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Tutorial: http://www.mdtutorials.com/gmx/index.html, https://tutorials.gromacs.org/
Learning outcomes:
Understanding the scope of MD simulations and the key considerations before setting up a simulation.
Hands-on experience on MD simulation using GROMACS.
Instructor: Nandan Haloi, PhD
About the instructor
Dr. Haloi is driven by a fundamental question: How do biomolecules work at the atomic level to power life? Combining molecular simulations, machine learning, and experimental data like cryo-EM and small-angle scattering, he unravels the intricate motions of proteins and their interactions with drugs. He is currently a Marie Skłodowska-Curie Actions Postdoctoral Fellow at KTH Royal Institute of Technology, under the mentorship of Prof. Erik Lindahl. He completed his PhD in Biophysics and Quantitative Biology with Emad Tajkhorshid in 2021 at the University of Illinois at Urbana-Champaign, Illinois, USA. His work has been recognized with prestigious awards and featured in top journals, reflecting his commitment to advancing science and mentoring future researchers. You can read more about his work on his personal webpage: https://nandanhaloi.netlify.app/
3-) Interoperable and Reproducible Biomolecular Simulation Workflows using BioExcel Building Blocks (BioBB)
Tools, libraries, and applications used: Python, Conda, and BioBB library.
Information about the library, installation protocols, and dependencies can be found here: https://mmb.irbbarcelona.org/biobb/;
All the tutorials are available here: https://mmb.irbbarcelona.org/biobb/workflows
Learning outcomes: Learn how to build FAIR (Findable, Accessible, Interoperable, and Reusable/Reproducible) biomolecular simulation workflows using the BioBB library.
Instructor: Adam Hospital
About the instructor: Adam Hospital is a Postdoctoral fellow at the Molecular Modeling and Bioinformatics Unit (MMB) – Institute for Research in Biomedicine in Barcelona (IRB-Barcelona) and research software engineer for the Spanish National Institute of Bioinformatics (INB, ELIXIR-ES). From a computer science background, he jumped to the bioinformatics world and got trapped by the fascinating field of structural bioinformatics. He has been involved in scientific projects at IRB and at the Barcelona Supercomputing Center (BSC), and he is currently leading the workflows team in the BioExcel CoE. While working as a bioinformatician, he obtained his PhD in Biotechnology from the University of Barcelona with his thesis “High Throughput Computational Studies of Macromolecular Structure Flexibility”. He has developed and coordinated a set of public web servers and databases related to macromolecular structure flexibility, included in the INB integrated platform for macromolecular flexibility.
4) Fundamentals and Practical Use Cases of Free Energy Calculations with PMX
Tools, libraries, and applications used: Conda and GROMACS.
The installation protocol and dependencies are documented here (http://pmx.mpibpc.mpg.de/Tutorial2024/Coimbra_2024/ligand_tutorial.html).
All the tutorials are available here: http://pmx.mpibpc.mpg.de/tutorial.html
Learning outcomes:
(i) the basics of free energy calculations
(ii) their use in predicting protein-ligand binding free energies with PMX and GROMACS, with direct relevance to drug design.
Instructor: Sudarshan Behera
About the instructor: Sudarshan Behera is a postdoctoral researcher in the Computational Biomolecular Dynamics group at the Max Planck Institute for Multidisciplinary Sciences, Goettingen. He is involved in developing methods for identifying and tackling convergence issues in non-equilibrium alchemical free energy calculations, as well as in the development of PMX software. Prior to this, whilst studying for his Ph.D. at JNCASR, Bangalore, India, he investigated the structure and dynamics of various enzymes using MD and enhanced sampling methods.
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Contact: ncc@ulakbim.gov.tr
This course is offered free of charge
Notes:
Participants will use their own laptop or computer for the hands-on sessions.
Before the training, participants will receive instructions on how to install the software and configure the environment.
The training consists of lectures and hands-on sessions. All registered participants will be able to follow the lectures; however, the hands-on sessions will have a limited capacity of 100 people (40 face-to-face particpants and 60 online participants). Based on the registration form, participants will be selected by considering their experience, area of research, and qualifications. Participants should meet the qualification requirements of the hands-on sessions. The acceptance notification will be sent at least 10 days before the event. Selected participants (for the hands-on sessions) will receive a temporary user account for the hands-on training.
Please note that the allocated compute time should only be used for running the hands-on examples.
Please note that only a limited technical support will be provided to online participants!
If you are unable to attend, please cancel your registration as soon as possible so that others may have the opportunity to benefit from the hands-on sessions.
Please note that a certificate of attendance will be given only to participants who will follow a minimum of 70% of the whole duration of the course and will be signed in with full name.
Please consider the time difference between EU countries and Türkiye.
Acknowledgements
This event was supported by the EuroCC 2 and EuroCC4SEE projects, which received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreements No. 101101903 and No. 101191697, respectively. The JU receives support from the Digital Europe Programme and Germany, Bulgaria, Austria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, Greece, Hungary, Ireland, Italy, Lithuania, Latvia, Poland, Portugal, Romania, Slovenia, Spain, Sweden, France, Netherlands, Belgium, Luxembourg, Slovakia, Norway, Türkiye, Republic of North Macedonia, Iceland, Montenegro, Serbia.
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