Publications

Browse recent abstracts here.

  1. Calcium Lockdown - Published 12 November 2025 in Journal of Structural Biology X (doi 10.1016/j.yjsbx.2025.100139): Calcium stabilizes the flexible N-terminal domain of the bacterial ion channel DeCLIC Chen Fan,° Marie Lycksell, Yuxuan Zhuang, Rebecca J Howard,° Erik Lindahl° Pentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some prokaryotic pLGICs contain… Continue reading Calcium Lockdown
  2. Discovering New States with AF2 + MD - Published 30 October 2025 in Communications Chemistry (doi 10.1038/s42004-025-01751-4): Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations Tatiana Shugaeva, Rebecca J Howard, Nandan Haloi,° Erik Lindahl° Modeling atomic coordinates into a target cryo-electron microscopy map is a crucial step in structure determination. Despite recent advances, proteins with multiple functional states remain… Continue reading Discovering New States with AF2 + MD
  3. Fitting Ligands with AF3 - Published 11 August 2025 in PLoS Computational Biology (doi 10.1371/journal.pcbi.1013367): Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics Nandan Haloi, Rebecca J Howard, Erik Lindahl Resolving protein-ligand interactions in atomic detail is key to understanding how small molecules regulate macromolecular function. Although recent breakthroughs in cryogenic electron microscopy (cryo-EM) have enabled high-quality reconstruction of… Continue reading Fitting Ligands with AF3
  4. Drugging rho1 - Published 1 August 2025 in Nature Communications (doi 10.1038/s41467-025-61932-6): Cryo-EM structures of ρ1 GABAA receptors with antagonist and agonist drugs Chen Fan,° John Cowgill, Rebecca J Howard,° Erik Lindahl° The family of ρ-type GABAA receptors includes potential therapeutic targets in several neurological conditions, and features distinctive pharmacology compared to other subtypes. Here we report four cryo-EM structures… Continue reading Drugging rho1
  5. Backbone Lock in GABA(A) - Published 3 July 2025 in Nature Communications (doi 10.1038/s41467-025-61447-0): A single main-chain hydrogen bond required to keep GABAA receptors closed Cecilia M Borghese, Jason D Galpin, Samuel Eriksson Lidbrink, Yuxuan Zhuang, Netrang G Desai, Rebecca J Howard, Erik Lindahl, Christopher A Ahern, Marcel P Goldschen-Ohm GABAA receptors (GABAARs) are the primary inhibitory neurotransmitter receptors throughout the central… Continue reading Backbone Lock in GABA(A)
  6. Building Ensembles with SAS and AF2 - Published 27 June 2025 in PLoS Computational Biology (doi 10.1371/journal.pcbi.1013187): Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold Samuel Eriksson Lidbrink, Rebecca J Howard, Nandan Haloi,° Erik Lindahl° The function of a protein is enabled by its conformational landscape. For non-rigid proteins, a complete characterization of this landscape requires… Continue reading Building Ensembles with SAS and AF2
  7. Engineering Lipid Binding - Version of Record 30 April 2025 in eLife (doi 10.7554/eLife.104237.3): Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization Mia L Abramsson, Robin A Corey,° Jan L Skerle, Louise J Persson, Olivia Andén, Abraham O Oluwole, Rebecca J Howard, Erik Lindahl, Carol V Robinson, Kvido Strisovsky, Erik G Marklund, David Drew,… Continue reading Engineering Lipid Binding
  8. Stimulants in a Cryptic Serotonin Pocket - Published 11 April 2025 in Science Advances (doi 10.1126/sciadv.adr0797): Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor Nandan Haloi, Emelia Karlsson, Mark Delarue, Rebecca J Howard,° Erik Lindahl° A diverse set of modulators, including stimulants and anesthetics, regulates ion channel function in our nervous system. However, structures… Continue reading Stimulants in a Cryptic Serotonin Pocket
  9. Stimulants in the Vestibule - Published 11 March 2025 in British Journal of Pharmacology (doi 10.1111/bph.70011): Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel Emelia Karlsson, Olivia Andén, Chen Fan, Zaineb Fourati, Ahmed Haouz, Yuxuan Zhuang, Rebecca J Howard, Marc Delarue, Erik Lindahl Background and Purpose Allosteric modulation of pentameric ligand-gated ion channels (pLGICs) are critical for the action of neurotransmitters and many psychoactive drugs.… Continue reading Stimulants in the Vestibule
  10. Computational Opening - Published 10 January 2025 in Science Advances (doi 10.1126/sciadv.adq3788): Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface Nandan Haloi, Samuel Eriksson Lidbrink, Rebecca J Howard, Erik Lindahl γ-Aminobutyric acid type A (GABAA) receptors are ligand-gated ion channels in the central nervous system with largely inhibitory function. Despite being a… Continue reading Computational Opening
  11. MSMs for alpha-7s - Published 18 October 2024 in Nature Communications (doi 10.1038/s41467-024-53170-z): Symmetry-adapted Markov state models of closing, opening, and desensitizing in α7 nicotinic acetylcholine receptors Yuxuan Zhuang, Rebecca J Howard, Erik Lindahl α7 nicotinic acetylcholine receptors (nAChRs) are homopentameric ligand-gated ion channels with critical roles in the nervous system. Recent studies have resolved and functionally annotated closed,… Continue reading MSMs for alpha-7s
  12. Steroids Here and There - Published 6 September 2024 in Nature Communications (doi 10.1038/s41467-024-51904-7): Divergent mechanisms of steroid inhibition in the human ρ1 GABAA receptor Chen Fan,* John Cowgill,* Rebecca J Howard,° Erik Lindahl° ρ-type γ-aminobutyric acid-A (GABAA) receptors are widely distributed in the retina and brain, and are potential drug targets for the treatment of visual, sleep and cognitive… Continue reading Steroids Here and There
  13. Across the MDverse - Published 30 August 2024 in eLife (doi 10.7554/elife.90061): MDverse, shedding light on the dark matter of molecular dynamics simulations Johanna K S Tiemann,* Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J Howard, Lucie Delemotte, Erik Lindahl, Marc Baaden, Kresten Lindorff-Larsen, Matthieu Chavent,* Pierre Poulain* The rise of open science and the absence of… Continue reading Across the MDverse
  14. Allosteric Contacts of Cholesterol - Published 15 May 2024 in the Journal of Physical Chemistry B (doi 10.1021/acs.jpcb.4c01703): Allosteric cholesterol site in glycine receptors characterized through molecular simulations Farzaneh Jalalypour, Rebecca J Howard, Erik Lindahl Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the… Continue reading Allosteric Contacts of Cholesterol
  15. TRP on Acid - Published 26 April 2024 in EMBO Journal (doi 10.1038/s44318-024-00106-4): Functional and structural insights into activation of TRPV2 by weak acids Ferdinand M Haug, Ruth A Pumroy, Akshay Sridhar, Sebastian Pantke, Florian Dimek, Tabea C Fricke, Axel Hage, Christine Herzog, Frank G Echtermeyer, Jeanne de la Roche, Adrian Koh, Abhay Kotecha, Rebecca J Howard, Erik Lindahl,… Continue reading TRP on Acid
  16. Simulating Biosensors - Published 1 February 2024 in Protein Engineering, Design and Selection (doi 10.1093/protein/gzae003): Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids Nandan Haloi*, Shan Huang*, Aaron L Nichols, Eve J Fine, Nicholas J Friesenhahn, Christopher B Marotta, Dennis A Dougherty, Erik Lindahl, Rebecca J Howard, Stephen… Continue reading Simulating Biosensors
  17. Multidisciplinary Lipid Discovery - Published 30 January 2024 in eLife (doi 10.7554/eLife.86016.3): Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM Cathrine Bergh, Urška Rovšnik, Rebecca J Howard, Erik Lindahl Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to… Continue reading Multidisciplinary Lipid Discovery
  18. Automating CpHMD - Published 12 January 2024 in The Journal of Chemical Information and Modeling (doi 10.1021/acs.jcim.3c01313): phbuilder: A tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev*, Berk Hess* Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby… Continue reading Automating CpHMD
  19. Resolving Rho1 - Published 1 September 2023 in Neuron (doi 10.1016/j.neuron.2023.08.006): Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor John Cowgill*, Chen Fan*, Nandan Haloi, Yuxuan Zhuang, Rebecca J Howard°, Erik Lindahl° The neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs).… Continue reading Resolving Rho1
  20. New Sites for Steroids - Published 22 August 2023 in Nature Communications (doi 10.1038/s41467-023-40800-1): Structural insights into opposing actions of neurosteroids on GABAA receptors Dagimhiwat H Legesse, Chen Fan, Jinfeng Teng, Yuxuan Zhuang, Rebecca J Howard, Colleen M Noviello, Erik Lindahl, Ryan E Hibbs γ-Aminobutyric acid type A (GABAA) receptors mediate fast inhibitory signaling in the brain and are targets… Continue reading New Sites for Steroids
  21. Density Fitting, Fast & Gentle - Published online 31 July 2023 in PLOS Computational Biology (doi 10.1371/journal.pcbi.1011255): Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach Christian Blau, Linnea Yvonnesdotter, Erik Lindahl Better detectors and automated data collection have generated a flood of high-resolution cryo-EM maps, which in turn has renewed interest in improving methods for determining… Continue reading Density Fitting, Fast & Gentle
  22. MD-Fitting a Membrane Protein - Published 11 July 2023 in Biophysical Journal (doi 10.1016/j.bpj.2023.05.033): Automated simulation-based membrane protein refinement into cryo-EM data Linnea Yvonnesdotter, Urška Rovšnik, Christian Blau, Marie Lycksell, Rebecca J Howard, Erik Lindahl The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins—a category that constitutes a disproportionate share of drug… Continue reading MD-Fitting a Membrane Protein
  23. Ivermectin by NMR - Published 23 February 2023 in ACS Chemical Neuroscience (doi 10.1021/acschemneuro.2c00783): Structural elucidation of ivermectin binding to α7nAChR and the induced channel desensitization Vasyl Bondarenko, Qiang Chen, Kevin Singewald, Nandan Haloi, Tommy S. Tillman, Rebecca J Howard, Erik Lindahl, Yan Xu, Pei Tang The α7 nicotinic acetylcholine receptor (α7nAChR) mediates signaling in the central nervous system and cholinergic anti-inflammatory pathways. Ivermectin is a positive… Continue reading Ivermectin by NMR
  24. Pi in the Gating Cycle of NavAb - Published 14 December 2022 in Journal of General Physiology (doi 10.1085/jgp.202213214): An α–π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb Koushik Choudhury, Rebecca J Howard, Lucie Delemotte Voltage-gated sodium channels play an important role in electrical signaling in excitable cells. In response to changes in membrane potential, they cycle… Continue reading Pi in the Gating Cycle of NavAb
  25. Divalents and Dynamic Domains - Published 8 December 2022 in Proceedings of the National Academy of Sciences of the USA (doi 10.1073/pnas.2210669119): Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel Marie Lycksell, Urška Rovšnik, Anton Hanke, Anne Martel, Rebecca J Howard, Erik Lindahl Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging… Continue reading Divalents and Dynamic Domains
  26. Lipid Sites in nAChR States - Published 17 October 2022 in Proceedings of the National Academy of Sciences of the USA (doi 10.1073/pnas.2208081119): Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators Yuxuan Zhuang, Colleen M Noviello, Ryan E Hibbs, Rebecca J Howard, Erik Lindahl The α7 nicotinic acetylcholine receptor is a pentameric… Continue reading Lipid Sites in nAChR States
  27. Modeling Bimodal Modulation - Published 6 August 2022 in Nature Communications (doi 10.1038/s41467-022-32212-4): Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities Shaotong Zhu, Akshay Sridhar, Jinfeng Teng, Rebecca J Howard, Erik Lindahl & Ryan E Hibbs γ-Aminobutyric acid type A (GABAA) receptors are pentameric ligand-gated ion channels abundant in the central nervous system and are prolific drug targets for treating anxiety, sleep… Continue reading Modeling Bimodal Modulation
  28. COVID-E Biophysics - Published 1 October 2022 in Biochimica et Biophysica Acta – Biomembranes (doi 10.1016/j.bbamem.2022.183994): Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium Aujan Mehregan, Sergio Pérez-Conesa, Yuxuan Zhuang, Ahmad Elbahnsi, Diletta Pasini, Erik Lindahl, Rebecca J Howard, Chris Ulens, Lucie Delemotte SARS-CoV-2 contains four structural proteins in its genome. These proteins… Continue reading COVID-E Biophysics
  29. Pi-Bulge to Open - Published 4 January 2022 in Biophysical Journal (doi 10.1016/j.bpj.2021.12.010): An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine Koushik Choudhury, Marina A Kasimova, Sarah McComas, Rebecca J Howard, Lucie Delemotte Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells.… Continue reading Pi-Bulge to Open
  30. From Leak to Disease - Published December 2021 in Journal of Biological Chemistry (doi 10.1016/j.jbc.2021.101355): A missense mutation converts the Na+,K+-ATPase into an ion channel and causes therapy-resistant epilepsy Sofia Ygberg, Evgeny E Akkuratov*, Rebecca J Howard*, Fulya Taylan, Daniel C Jans*, Dhani R Mahato, Adriana Katz, Paula F Kinoshita, Benjamin Portal, Inger Nennesmo, Maria Lindskog, Steven JD Karlish, Magnus… Continue reading From Leak to Disease
  31. MSMs for Proton Gating - Published 15 October 2021 in eLife (doi 10.7554/eLife.68369): Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel Cathrine Bergh, Stephanie A Heusser, Rebecca Howard, Erik Lindahl Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels the details of gating remain… Continue reading MSMs for Proton Gating
  32. Tracking Protons with Neutrons - Published 14 September 2021 in Proceedings of the National Academy of Sciences of the USA (doi 10.1073/pnas.2108006118): Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering Marie Lycksell, Urška Rovšnik, Cathrine Bergh, Nicolai T. Johansen, Anne Martel, Lionel Porcar, Lise Arleth, Rebecca J Howard, Erik Lindahl Pentameric ligand-gated ion channels undergo subtle conformational cycling to control electrochemical signal… Continue reading Tracking Protons with Neutrons
  33. Proton Gating by CryoEM - Available online 1 July 2021 in Life Science Alliance (doi 10.26508/lsa.202101011): Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations Urška Rovšnik, Yuxuan Zhuang, Björn O Forsberg, Marta Carroni, Linnea Yvonnesdotter, Rebecca J Howard, Erik Lindahl  Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies… Continue reading Proton Gating by CryoEM
  34. Illuminating pLGICs - Available online 3 July 2021 in the Journal of Molecular Biology (doi 10.1016/j.jmb.2021.167128): Elephants in the dark: insights and incongruities in pentameric ligand-gated ion channel models Rebecca J Howard The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets… Continue reading Illuminating pLGICs
  35. Cation-π Lipid-Channel Binding - Available online 19 June 2021 in the Journal of Biological Chemistry (doi 10.1016/j.jbc.2021.100899): Regulation of a pentameric ligand-gated ion channel by a semi-conserved cationic-lipid binding site Akshay Sridhar*, Sarah CR Lummis*, Diletta Pasini, Aujan Mehregan, Marijke Brams, Kumiko Kambara, Daniel Bertrand, Erik Lindahl, Rebecca J Howard, Chris Ulens Pentameric ligand-gated ion channels (pLGICs) are crucial… Continue reading Cation-π Lipid-Channel Binding
  36. Trends in Ion-Channel MD - Available online 30 April 2021 in Trends in Biochemical Sciences (doi 10.1016/j.tibs.2021.04.005): Molecular dynamics simulations of ion channels Vincenzo Carnevale*, Lucie Delemotte*, Rebecca J Howard* Propelled by enormous increases in computational power, molecular dynamics (MD) simulations were first reported in 1957 by B.J. Alder and T.E. Wainwright and since then have moved from this proof… Continue reading Trends in Ion-Channel MD
  37. Drugging COVID-19 with Dynamics - Published 16 March 2021 in ACS Pharmacology & Translational Sciences (doi 10.1021/acsptsci.0c00215): A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics Jonas Gossen, Simone Albani, Anton Hanke, Benjamin P Joseph, Cathrine Bergh, Maria Kuzikov, Elisa Costanzi, Candida Manelfi, Paola Storici, Philip Gribbon, Andrea R Beccari,… Continue reading Drugging COVID-19 with Dynamics
  38. Homegrown Tests for COVID-19 - Published 19 January 2021 in Scientific Reports (doi 10.1038/s41598-020-80352-8): Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples Alisa Alekseenko, Donal Barrett, Yerma Pareja-Sanchez, Rebecca J Howard, Emilia Strandback, Henry Ampah-Korsah, Urška Rovšnik, Silvia Zuniga-Veliz, Alexander Klenov, Jayshna Malloo, Shenglong Ye, Xiyang Liu, Björn Reinius, Simon J. Elsässer, Tomas Nyman, Gustaf Sandh, Xiushan… Continue reading Homegrown Tests for COVID-19
  39. Speedier Simulations with Parallelization - Published 5 October 2020 in The Journal of Chemical Physics (doi 10.1063/5.0018516): Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS Szilárd Páll, Artem Zhmurov, Paul Bauer, Mark Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular… Continue reading Speedier Simulations with Parallelization
  40. Fungal Metabolism at its Core - Published 16 September 2020 in Nature Communications (doi 10.1038/s41467-020-18401-z): Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex Björn O Forsberg, Shintaro Aibara, Rebecca J Howard, Narges Mortezaei, Erik Lindahl The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar… Continue reading Fungal Metabolism at its Core
  41. Unveiling Valium - Published 2 September 2020 in Nature (doi 10.1038/s41586-020-2654-5): Shared structural mechanisms of general anaesthetics and benzodiazepines Jeong Joo Kim, Anant Gharpure, Jinfeng Teng, Yuxuan Zhuang, Rebecca J Howard, Shaotong Zhu, Colleen M Noviello, Richard M Walsh Jr, Erik Lindahl, Ryan E Hibbs Most general anaesthetics and classical benzodiazepine drugs act through positive modulation of γ-aminobutyric… Continue reading Unveiling Valium
  42. Dramatic Domains of DeCLIC - Published 16 June 2020 in Proceedings of the National Academy of Sciences of the USA (v. 117 pp. 13437–13446): Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel Haidai Hu, Rebecca J Howard, Ugo Bastolla, Erik Lindahl, Marc Delarue Pentameric ligand-gated ion channels (pLGICs) are allosteric receptors that mediate rapid electrochemical signal transduction in the… Continue reading Dramatic Domains of DeCLIC
  43. Library Building for CryoEM - Published 1 April 2020 in Acta Crystallographica Section D (v. 76 pp. 350–356): Development of basic building blocks for cryo-EM: the emcore and emvis software libraries José Miguel de la Rosa-Trevín, Pedro Alberto Hernández Viga, Joaquín Otónc, Erik Lindahl Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are… Continue reading Library Building for CryoEM
  44. Models for MD Sharing - Published 17 September 2019 in the Journal of Chemical Information and Modeling (v. 59 pp. 4093–4099): Sharing data from molecular simulations Mark Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre MJJ Bonvin, Matthieu Chavent, John Chodera, Karmen Čondić-Jurkić, Lucie Delemotte, Helmut Grubmüller, Rebecca J Howard, E Joseph Jordan, Erik Lindahl, OH Samuli Ollila,… Continue reading Models for MD Sharing
  45. Nicotinic Structure & Dynamics - For the November 2019 issue of Neuron (v. 104 pp. 501–511.e6): Agonist selectivity and ion permeation in the α3β4 ganglionic nicotinic receptor Anant Gharpure, Jinfeng Teng, Yuxuan Zhuang, Colleen M. Noviello, Richard M. Walsh Jr., Rico Cabuco, Rebecca J. Howard, Nurulain T. Zaveri, Erik Lindahl, Ryan E. Hibbs Nicotinic acetylcholine receptors are pentameric ion channels… Continue reading Nicotinic Structure & Dynamics
  46. Elastic Networks on the Net - For the September 2019 issue of Bioinformatics (v. 35 pp. 3505–3507): eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces Laura Orellana, Johan Gustavsson, Cathrine Bergh, Ozge Yoluk, Erik Lindahl Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial.… Continue reading Elastic Networks on the Net
  47. Reproducibility rules - Released 17 January 2019 in PLOS Computational Biology (v. 15 art. e1006649): Ten simple rules on how to create open access and reproducible molecular simulations of biological systems Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist All PLOS journals have an open data policy that, amongst other things, states… Continue reading Reproducibility rules
  48. e-Science in Scandinavia - From the December 2018 release of Informatik Spektrum (v. 41 pp. 398–404): e-Science in Scandinavia: The Case of the Swedish e-Science Research Center Olivia Eriksson, Erwin Laure, Erik Lindahl, Dan Henningson & Anders Ynnerman The Swedish e-Science Research Centre (SeRC) is based on a collaboration between four Swedish universities: The KTH Royal Institute of Technology (KTH), Stockholm University (SU), Karolinska Institutet… Continue reading e-Science in Scandinavia
  49. RELION Refined - Accepted manuscript, posted ahead of online November 9, 2018 in eLife (v. 7 art. e42166): New tools for automated high-resolution cryo-EM structure determination in RELION-3 Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim JH Hagen, Erik Lindahl & Sjors HW Scheres Here, we describe the third major release of RELION. CPU-based vector acceleration has been… Continue reading RELION Refined
  50. Dynamic Basis for Drug Binding - From the October 16, 2018 issue of Proceedings of the National Academy of Sciences of the USA (v. 115 pp. 10672–10677): Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity Stephanie A Heusser, Marie Lycksell, Xueqing Wang, Sarah E McComas, Rebecca J Howard & Erik Lindahl Molecular mechanisms… Continue reading Dynamic Basis for Drug Binding
  51. Who Dances With an Electric Beat? - For the October 1, 2018 issue of the Journal of General Physiology (v. 150 art. 1444): Determining the molecular basis of voltage sensitivity in membrane proteins Marina A. Kasimova, Erik Lindahl & Lucie Delemotte Voltage-sensitive membrane proteins are united by their ability to transform changes in membrane potential into mechanical work. They are responsible for a… Continue reading Who Dances With an Electric Beat?
  52. Frozen in Motion - From the June 1, 2018 release of eLife (v. 7 art. e36861): Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION Takanori Nakane, Dari Kimanius, Erik Lindahl & Sjors HW Scheres Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe… Continue reading Frozen in Motion
  53. Consciousness Crystallized - Featured on the April 24, 2018 cover of Cell Reports (v. 23 pp. 993–1004): Structural basis for a bimodal allosteric mechanism of general anesthetic modulation in pentameric ligand-gated ion channels Zaineb Fourati*, Rebecca J Howard*, Stephanie A Heusser, Haidai Hu, Reinis R Ruza, Ludovic Sauguet, Erik Lindahl** & Marc Delarue** *Equal contributions; **senior authors Ion channel… Continue reading Consciousness Crystallized
  54. Review: Permeating Disciplines - From the April 2018 release of Biochimica et Biophysica Acta – Biomembranes (v. 1860 pp. 927–942): Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport Rebecca J Howard, Vincenzo Carnevale, Lucie Delemotte, Ute A Hellmich & Brad S Rothberg Ion translocation across biological barriers is a fundamental requirement for life. In… Continue reading Review: Permeating Disciplines