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Srini Chari, Founder of Cabot Partners, an IT analyst and consulting firm, talks about the benefits of Intel® Omni-Path Fabric, which balances overall system performance, and addresses the needs of tomorrow’s high-performance computing. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well … (2020) Nature. Lars Norlén, Assoc. Development of basic building blocks for cryo-EM: the emcore and emvis software libraries. Verified email at scilifelab.se - Homepage. Then experts from abroad, including Marta Carroni, were recruited to enable the Swedish academic community to start benefiting from the advances. In this video from the Intel HPC Developer Conference, Erik Lindahl from Stockholm University describes the challenges of cryo-EM, a technique that fires beams of electrons at proteins that have been frozen in solution, to deduce the biomolecules’ structure. Movements are indicated by arrows. Coronavirus: ... Swedish e-Science Research Centre to Erik Lindahl. Available from: 2020-04-01 Created: 2020-03-10 Last updated: 2020-05-25 Bibliographically approved List of papers 1. b Orientation of the DNA duplex with respect to the PCNA threefold symmetry axis. At the University of Stockholm, NVIDIA GPUs enable researcher Erik Lindahl’s RELION imaging application to process and reconstruct 3D images of molecular structures. CCP-EM Erik Lindahl | Spring Symposium 2017 Collaborative Computational Project for Electron Cryo-Microscopy Spring Symposium 2017 Speakers: Erik Lindahl, Carolyn Moores, Morgan Beeby, Tanmay Bharat, Tristan Croll, Maya Topf, David Waterman, Paul Adams, Rob Nicholis, Becky Thompson, Austra Domanska, Colin Palmer, Piet Gros, Kay Grunewald More details: https://www.simonsfoundation.org/event/nyc-computational-cryo-em-summer-workshop/ This assumption no longer holds in the presence of continuous structural heterogeneity in the data set. Sort. eLife (2018) 7: e36861. Professor Erik Lindahl of Stockholm University and Professor Sjors Scheres of the UK MRC Laboratory of Molecular Biology have worked with Intel to reduce Cryo-EM image reconstruction times from as many as 47 hours to as few as 5.6 hours through redesigned algorithms and optimized code 4. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. (2020) Science. Stockholm University Professor Erik Lindahl discusses the new era of structural biology and how RELION and Intel® technology help optimize Cryo-EM* models to extract more data for 3D protein structures. He has authored some 130 scientific publications and is the recipient of an ERC starting grant. Cryo-EM lets researchers freeze molecules in mid-motion and see biological processes at the atomic level for the first time. The … Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2 | Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl | Biology, Cryo-EM, CUDA, Image processing, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980 Ti SHWS: Reviewing editor, eLife. Lindahl’s research is focused on understanding the molecular mechanisms of membrane proteins, in particular ion channels, through a combination of molecular simulations and experimental work involving cryo-EM and electrophysiology. At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript. Erik Lindahl. The other authors declare that no competing interests exist. b Shared structural features between archaeal PolD and eukaryotic Polα C-terminal regions. Free to read & use . The main assumption in conventional cryo-EM single-particle analysis is that every experimental particle image is a two-dimensional projection of a common three-dimensional structure. José Miguel de la Rosa-Trevín, Pedro Alberto Hernández Viga, Joaquín Otónc, Erik Lindahl. Within the frame of joint development of bilateral projects between Sweden and South Korea, SciLifeLab scientists from Stockholm University Alexey Amunts’, Erik Lindahl’s labs and cryo-EM facility trained over 200 students and postdocs in four cities in South Korea. In this video from the Intel HPC Developer Conference, Erik Lindahl from Stockholm University describes the challenges of cryo-EM, a technique that fires beams of electrons at proteins that have been frozen in solution, to deduce the biomolecules’ structure. Features from selected parts of experimental cryo-EM images ( d ) can then be compared to features present in the simulated cryo-EM images ( e ), or toward a negative control such as water ( c and f ). Go to: Additional information. Date: May 12 - 16, 2020 Location: Clarion Hotel Sign, Stockholm, Sweden. Backbone traces of the DP2 cryo-EM structure and the DP2 (1–1061) crystal structure are shown in blue and black, respectively. 12. The training workshops included 40 hours of lectures and practical work in […] Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine. Organized in collaboration with Science for Life Laboratory Sponsored by Thermo Fisher Scientific Inc. For important information on the coronavirus, please click here. English: a Structural comparison of the P. abyssi PolD DP1-DP2(1093–1216) region of the cryo-EM structure with the Homo sapiens Polα POLA2-POLA1(1319–1456) crystal structure (PDB ID: 5EXR). Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation. Two versions of the cryo-EM refinement program have been implemented: the first one accepts classical crystallographic space groups, and the second one assumes there exist some internal symmetry in the object to be fitted in the cryo-EM Professor of Biophysics, Science for Life Laboratory, Stockholm University. (A) Movements of the DPBB-1, KH-like, and accessory-1 domains observed between the DP2 (1–1061) crystal structure (PDB ID: 5IJL ) and the PolD cryo-EM structure, supported by the cryo-EM density contoured at 6 σ (gray). "Structural basis of transcription-translation coupling" Chengyuan Wang, Vadim Molodtsov, Emre Firlar, Jason Kaelber, Gregor Blaha, Min Su, and Richard H. Ebright. To compare to experimental cryo-EM data (a), the unit cell of the all-atom structure was extended in three dimensions (b) and subjected to a cryo-EM simulation. Author … doi: 10.7554/eLife.36861; Forsberg BO, Aibara S, Kimanius D, Paul B, Lindahl E, Amunts A. Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h. Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. structure factors of the cryo-EM map, using CCP4 tools (26). English: a Two orthogonal views of the cryo-EM density map (left) and cartoon representations (right) of the DNA-bound PolD–PCNA complex. (2019) ... Rebecca J. Howard, Shaotong Zhu, Colleen Noviello, Richard M. Walsh Jr, Erik Lindahl, Ryan E. Hibbs. Lindahl, Erik, Professor. Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Swedish National Infrastructure for Computing 2015/16-45 to Erik Lindahl. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. RELION is the imaging software of the Nobel Prize-winning cryogenic electron microscope. Instead, multi-body refinement assumes that the continuous structural heterogeneity can be modelled … Note. Title. José Miguel de la Rosa-Trevín, Pedro Alberto Hernández Viga, Joaquín Otón, Erik Lindahl, Development of basic building blocks for cryo-EM: the emcore and emvis software libraries , Acta Crystallographica Section D Structural Biology, 10.1107/S2059798320003769, 76, 4, (350-356), (2020). Computational biophysics membrane proteins bioinformatics molecular simulation electrophysiology. Bjo¨rn O. Forsberg,‡ Shintaro Aibara,‡ Dari Kimanius,‡ Bijoya Paul, Erik Lindahl* and Alexey Amunts* Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden. RESEARCH ARTICLE Structure of the human ClC-1 chloride channel Kaituo Wang ID 1,2,3, Sarah Spruce Preisler ID 4, Liying Zhang1, Yanxiang Cui ID 2,3, Julie Winkel Missel1, Christina Grønberg ID 1, Kamil Gotfryd1, Erik Lindahl ID 5, Magnus Andersson ID 6, Kirstine Calloe ID 7, Pascal F. Egea8, Dan Arne Klaerke7, Michael Pusch ID 9, Per Amstrup Pedersen ID 4*, Z. Hong Zhou ID Organizer(s): Hongwei Wang, Nieng Yan, Claudio Ciferri and Erik Lindahl . MEETING CANCELLED: Cryo-EM for Health Science. Competing interests. 2018 Nov 9 ... Dari Kimanius 2 , Wim Jh Hagen 3 4 , Erik Lindahl 2 5 , Sjors Hw Scheres 1 Affiliations 1 MRC Laboratory of Molecular Biology, Cambridge, United Kingdom. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Cited by. Within the frame of joint development of bilateral projects between Sweden and South Korea, SciLifeLab scientists from the labs of Alexey Amunts and Erik Lindahl, as well as the cryo-EM facility, trained over 200 students and postdocs in four Universities in South Korea. Conserved α-helices and Zn-binding domain are shown in blue and green, respectively. Professor, Ph.D. 20 years research experience with focus on determining the skin structure using cryo-EM which, together with his career as a dermatologist, gives him an unique understanding of the skin’s structure. "Introducing the Pacific Northwest Center for Cryo-EM" Craig Yoshioka. Stockholm University Professor Erik Lindahl discusses the new era of structural biology and how RELION and Intel® technology help optimize Cryo-EM* models to extract more data for 3D protein structures. Cited by. Coronavirus: ... Lindahl E, 0000-0002-2734-2794, KTH Royal Institute of Technology; Scheres SH, 0000-0002-0462-6540, MRC Laboratory of Molecular Biology; Elife, 09 Nov 2018, 7 DOI: 10.7554/elife.42166 PMID: 30412051 PMCID: PMC6250425. Sort by citations Sort by year Sort by title. Erik Lindahl, Cyril Azuara, Patrice Koehl, Marc Delarue, NOMAD-Ref: ... For cryo-EM data, a phased correlation coefficient involving F.F * products (with F the complexe structure factor and F * its complex conjugate) are used instead of the X-ray correlation coefficient, which uses only structure factor amplitudes. New tools for automated high-resolution cryo-EM structure determination in RELION-3. New tools for automated high-resolution cryo-EM structure determination in RELION-3 Elife. Journal of ... Marijke Brams, Radovan Spurny, Steve Peigneur, Jan Tytgat, Erik Lindahl, Chris Ulens. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Erik Lindahl, a group leader at Stockholm University, jointly with Sjors Scheres from Cambridge developed accelerated software for 3D reconstruction that was readily applied. Articles Cited by. 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