BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Exploring Biomolecular Modeling and Simulations DTSTART:20250409T060000Z DTEND:20250410T140000Z DTSTAMP:20260511T020900Z UID:indico-event-177@indico.truba.gov.tr CONTACT:ncc@ulakbim.gov.tr DESCRIPTION:\n\nAll recordings of the training is published on NCC Türkiy e YouTube channel.\n\nOrganisation: BioExcel\, NCC Sweden\, and NCC Türk iye in the context of CASTIEL 2 "Training Sprint" Initiative\n\nDate: Apr il 9-10\, 2025\n\nRegistration Deadline: 24 March 2025\n\nEvent Type: Tra ining\n\nFormat: Hybrid (on-site & online) \n\nSkill Level: Intermedia te \n\nLanguage: English\n\nPrerequisites: \n\n-Experience in a Linux e nvironment\, jupyter notebook\, Python\, Conda\, and BioBB library. \n\n- Familiarity with High-Performance Computing (HPC) systems is required for participation in the hands-on sessions.\n\n-The training is primarily desi gned for participants from academia (with at least a graduate degree)\, in dustry\, or public administration who are using or planning to use biomole cular modeling and simulation in their research.\n\n-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 off icial email addresses are accepted for registration\; personal or generic emails are not permitted.\n\nFor the event programme see the timetable sec tion. \n\nThe training consists of four sessions: \n\n1-) Integrative mo deling of biomolecular complexes with HADDOCK\n\nTools\, libraries\, and a pplications used:\n\nHADDOCK3: https://github.com/haddocking/haddock3\n\n HADDOCK web server: https://wenmr.science.uu.nl\n\nHADDOCK tutorials: ht tps://bonvinlab.org/education\n\nLearning outcomes: \n\nGetting insights into the field of integrative modeling and more specifically into HADDOCK. \n\nGaining hands-on experience in the modeling of biomolecular complexes with HADDOCK\n\nInstructor: Alexandre M.J.J Bonvin\n\nAbout the instructo r: Alexandre Bonvin (1964) studied Chemistry at Lausanne University\, Swi tzerland and obtained his PhD at Utrecht University in the Netherlands (19 93). After two post-doc periods at Yale University (USA) and the ETHZ (CH)  he joined Utrecht University in 1998 where he was appointed full profess or of computational structural biology in 2009. In 2006\, he received a p restigious VICI grant from the Dutch Research Council. He was director of chemical education (2009-2012)\, vice head of the Chemistry Department (2 010-2012) and Scientific Director of the Bijvoet Centre for Biomolecular R esearch (2019-2023). He has and is participating to several EU projects in cluding the BioExcel Center of Excellence in Biomolecular Simulations. Hi s work has resulted in over 275 peer-reviewed publications.\n\nResearch wi thin his group focuses on the development of reliable bioinformatics and c omputational approaches to predict\, model and dissect biomolecular intera ctions at atomic level. For this\, bioinformatics data\, structural inform ation and available biochemical or biophysical experimental data are combi ned to drive the modelling process. This is implemented and further develo ped in the widely used HADDOCK software for the modelling of biomolecular complexes (http://bonvinlab.org/software).\n\n2-) Molecular Dynamics Si mulations – GROMACS\n\nTools\, libraries\, and applications used: \n\n GROMACS: https://www.gromacs.org/\n\nVMD: https://www.ks.uiuc.edu/Develo pment/Download/download.cgi?PackageName=VMD\n\nTutorial: http://www.mdtut orials.com/gmx/index.html\, https://tutorials.gromacs.org/\n\nLearning ou tcomes: \n\nUnderstanding the scope of MD simulations and the key conside rations before setting up a simulation.\n\nHands-on experience on MD simul ation using GROMACS.\n\nInstructor: Nandan Haloi\, PhD\n\nAbout the instr uctor\n\nDr. Haloi is driven by a fundamental question: How do biomolecule s work at the atomic level to power life? Combining molecular simulations\ , machine learning\, and experimental data like cryo-EM and small-angle sc attering\, he unravels the intricate motions of proteins and their interac tions with drugs. He is currently a Marie Skłodowska-Curie Actions Postdo ctoral 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 Ur bana-Champaign\, Illinois\, USA. His work has been recognized with prestig ious awards and featured in top journals\, reflecting his commitment to ad vancing science and mentoring future researchers. You can read more about his work on his personal webpage: https://nandanhaloi.netlify.app/\n\n3-) Interoperable and Reproducible Biomolecular Simulation Workflows using Bi oExcel Building Blocks (BioBB)\n\nTools\, libraries\, and applications use d: Python\, Conda\, and BioBB library. \n\nInformation about the library\ , installation protocols\, and dependencies can be found here: https://mm b.irbbarcelona.org/biobb/\; \n\nAll the tutorials are available here: htt ps://mmb.irbbarcelona.org/biobb/workflows \n\nLearning outcomes: Learn h ow to build FAIR (Findable\, Accessible\, Interoperable\, and Reusable/Rep roducible) biomolecular simulation workflows using the BioBB library. \n \nInstructor: Adam Hospital \n\nAbout the instructor: Adam Hospital is a Postdoctoral fellow at the Molecular Modeling and Bioinformatics Unit ( MMB) – Institute for Research in Biomedicine in Barcelona (IRB-Barcelo na) 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 fie ld of structural bioinformatics. He has been involved in scientific projec ts at IRB and at the Barcelona Supercomputing Center (BSC)\, and he is cu rrently leading the workflows team in the BioExcel CoE. While working as a bioinformatician\, he obtained his PhD in Biotechnology from the Univers ity of Barcelona with his thesis “High Throughput Computational Studies of Macromolecular Structure Flexibility”. He has developed and coordinat ed a set of public web servers and databases related to macromolecular str ucture flexibility\, included in the INB integrated platform for macromol ecular flexibility.\n\n4) Fundamentals and Practical Use Cases of Free Ene rgy Calculations with PMX \n\nTools\, libraries\, and applications used:  Conda and GROMACS. \n\nThe installation protocol and dependencies are docu mented here (http://pmx.mpibpc.mpg.de/Tutorial2024/Coimbra_2024/ligand_tut orial.html).\n\nAll the tutorials are available here: http://pmx.mpibpc.m pg.de/tutorial.html\n\nLearning outcomes: \n\n(i) the basics of free ener gy calculations\n\n(ii) their use in predicting protein-ligand binding fre e energies with PMX and GROMACS\, with direct relevance to drug design.   \n\nInstructor: Sudarshan Behera\n\nAbout the instructor: Sudarshan Be hera is a postdoctoral researcher in the Computational Biomolecular Dynami cs group at the Max Planck Institute for Multidisciplinary Sciences\, Goet tingen. 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 st udying for his Ph.D. at JNCASR\, Bangalore\, India\, he investigated the s tructure and dynamics of various enzymes using MD and enhanced sampling me thods.\n\n......\n\nContact: ncc@ulakbim.gov.tr\n\nThis course is offered free of charge\n\nNotes:\n\nParticipants will use their own laptop or com puter for the hands-on sessions.\n\nBefore the training\, participants wil l receive instructions on how to install the software and configure the en vironment.\n\n\nThe training consists of lectures and hands-on sessions. A ll 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 registratio n form\, participants will be selected by considering their experience\, a rea of research\, and qualifications. Participants should meet the qualifi cation 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 hand s-on training. \n\nPlease note that the allocated compute time should onl y be used for running the hands-on examples. \n\nPlease note that only a limited technical support will be provided to online participants!\n\nIf y ou are unable to attend\, please cancel your registration as soon as possi ble so that others may have the opportunity to benefit from the hands-on s essions.\n\nPlease note that a certificate of attendance will be given onl y to participants who will follow a minimum of 70% of the whole duration o f the course and will be signed in with full name. \n\nPlease consider th e time difference between EU countries and Türkiye.\n\nAcknowledgements\n \n        \n\nThis event was supported by the EuroCC 2 and EuroCC4SE E projects\, which received funding from the European High-Performance Com puting 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 Rep ublic\, Denmark\, Estonia\, Finland\, Greece\, Hungary\, Ireland\, Italy\, Lithuania\, Latvia\, Poland\, Portugal\, Romania\, Slovenia\, Spain\, Swe den\, France\, Netherlands\, Belgium\, Luxembourg\, Slovakia\, Norway\, T ürkiye\, Republic of North Macedonia\, Iceland\, Montenegro\, Serbia.\n\n \nFollow us on Twitter and LinkedIn. Subscribe to our YouTube Channel!\n\n https://twitter.com/EuroCC_Turkey\n\nhttps://www.linkedin.com/company/euro cc-turkey\n\nhttps://www.youtube.com/channel/UC-qaWnbbTl6OPiPasUf4t8w/play lists\n\nhttps://indico.truba.gov.tr/event/177/ LOCATION:Room number:104-105 (Sabancı DX Digital Campus\, İstanbul) URL:https://indico.truba.gov.tr/event/177/ END:VEVENT END:VCALENDAR