Lindahl E

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Family name Lindahl
Given name Erik
Initials E
ORCID

ORCID 0000-0002-2734-2794
Affiliations

72 publications

PubMed DOI Crossref
Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.
Shugaeva T, Howard RJ, Haloi N, Lindahl E
Commun Chem 8 (1) 317 [2025-10-30; online 2025-10-30]
PubMed DOI Crossref
Cryo-EM structures of ρ1 GABAA receptors with antagonist and agonist drugs.
Fan C, Cowgill J, Howard RJ, Lindahl E
Nat Commun 16 (1) 7077 [2025-08-01; online 2025-08-01]
PubMed DOI Crossref
Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.
Haloi N, Howard RJ, Lindahl E
PLoS Comput Biol 21 (8) e1013367 [2025-08-00; online 2025-08-11]
PubMed DOI Crossref
Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold.
Lidbrink SE, Howard RJ, Haloi N, Lindahl E
PLoS Comput Biol 21 (6) e1013187 [2025-06-00; online 2025-06-27]
PubMed DOI Crossref
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor.
Haloi N, Karlsson E, Delarue M, Howard RJ, Lindahl E
Sci Adv 11 (15) eadr0797 [2025-04-11; online 2025-04-11]
DOI Crossref
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
- - (-) - [2025-03-26; online 2025-03-26]
DOI Crossref
Author response: Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
- - (-) - [2025-03-26; online 2025-03-26]
DOI Crossref
Structure and dynamics of a multidomain ligand-gated ion channel revealed under acidic conditions
Andén O, Rovšnik U, Lycksell M, ..., Howard RJ, Lindahl E
- - (-) - [2025-02-27; online 2025-02-27]
DOI Crossref
Calcium stabilization of a flexible N-terminal domain in a pentameric ligand-gated ion channel
Fan C, Lycksell M, Zhuang Y, Howard RJ, Lindahl E
- - (-) - [2025-02-27; online 2025-02-27]
DOI Crossref
Cryo-EM ligand building using generative AI and molecular dynamics
Haloi N, Howard RJ, Lindahl E
- - (-) - [2025-02-12; online 2025-02-12]
DOI Crossref
Modeling cryo-EM structures in alternative states with generative AI and density-guided simulations
Shugaeva T, Howard RJ, Haloi N, Lindahl E
- - (-) - [2025-02-08; online 2025-02-08]
DOI Crossref
Author response: Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
- - (-) - [2025-01-16; online 2025-01-16]
DOI Crossref
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Abramsson ML, Corey RA, Škerle J, ..., Stansfeld PJ, Landreh M
- - (-) - [2025-01-16; online 2025-01-16]
PubMed DOI Crossref
Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface.
Haloi N, Eriksson Lidbrink S, Howard RJ, Lindahl E
Sci Adv 11 (2) eadq3788 [2025-01-10; online 2025-01-08]
DOI Crossref
Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold
Lidbrink SE, Howard R, Haloi N, Lindahl E
- - (-) - [2024-09-07; online 2024-09-07]
DOI Crossref
MDverse, shedding light on the dark matter of molecular dynamics simulations
Tiemann JK, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
Elife 12 (-) - [2024-08-30; online 2024-08-30]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
MDverse, shedding light on the dark matter of molecular dynamics simulations.
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
Elife 12 (-) - [2024-08-30; online 2024-08-30]
PubMed DOI Crossref
Allosteric inhibition of CFTR gating by CFTRinh-172 binding in the pore.
Gao X, Yeh HI, Yang Z, ..., Kappes JC, Hwang TC
Nat Commun 15 (1) 6668 [2024-08-06; online 2024-08-06]
DOI Crossref
Cryo-EM structures of ρ1 GABA A receptors with antagonist and agonist drugs
Fan C, Cowgill J, Howard RJ, Lindahl E
- - (-) - [2024-07-30; online 2024-07-30]
PubMed DOI Crossref
Simulating the Skin Permeation Process of Ionizable Molecules.
Lundborg M, Wennberg C, Lindahl E, Norlén L
J Chem Inf Model 64 (13) 5295-5302 [2024-07-08; online 2024-06-25]
DOI Crossref
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
- - (-) - [2024-07-01; online 2024-07-01]
DOI Crossref
Author response: MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
- - (-) - [2024-07-01; online 2024-07-01]
PubMed DOI Crossref
Allosteric Cholesterol Site in Glycine Receptors Characterized through Molecular Simulations.
Jalalypour F, Howard RJ, Lindahl E
J Phys Chem B 128 (20) 4996-5007 [2024-05-23; online 2024-05-15]
DOI Crossref
Adaptive sampling-based structural prediction reveals opening of a GABA receptor through the αβ interface
Haloi N, Howard RJ, Lindahl E
- - (-) - [2024-05-05; online 2024-05-05]
DOI Crossref
GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability
Alekseenko A, Páll S, Lindahl E
- - (-) 71-84 [2024-05-05; online 2025-08-15]
PubMed DOI Crossref
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations.
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
bioRxiv - (-) - [2024-05-03; online 2024-05-03]
DOI Crossref
An Allosteric Cholesterol Site in Glycine Receptors Characterized Through Molecular Simulations
Jalalypour F, Howard RJ, Lindahl E
- - (-) - [2024-03-06; online 2024-03-06]
PubMed DOI Crossref
Structural basis for the oligomerization-facilitated NLRP3 activation.
Yu X, Matico RE, Miller R, ..., Van Opdenbosch N, Sharma S
Nat Commun 15 (1) 1164 [2024-02-07; online 2024-02-07]
PubMed DOI Crossref
Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM.
Bergh C, Rovšnik U, Howard R, Lindahl E
Elife 12 (-) - [2024-01-30; online 2024-01-30]
DOI Crossref
Divergent mechanisms of steroid inhibition in the human ρ1 GABA A receptor
Fan C, Cowgill J, Howard RJ, Lindahl E
- - (-) - [2024-01-26; online 2024-01-26]
PubMed DOI Crossref
Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids.
Haloi N, Huang S, Nichols AL, ..., Mayo SL, Lester HA
bioRxiv - (-) - [2024-01-18; online 2024-01-18]
DOI Crossref
Author Response: Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
Bergh C, Rovšnik U, Howard RJ, Lindahl E
- - (-) - [2024-01-05; online 2024-01-05]
DOI Crossref
Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
Bergh C, Rovšnik U, Howard RJ, Lindahl E
- - (-) - [2024-01-05; online 2024-01-05]
DOI Crossref
Symmetry-adapted Markov state models of closing, opening, and desensitizing in α7 nicotinic acetylcholine receptors
Zhuang Y, Howard RJ, Lindahl E
- - (-) - [2023-12-05; online 2023-12-05]
DOI Crossref
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT 3 A receptor
Haloi N, Karlsson E, Delarue M, Howard RJ, Lindahl E
- - (-) - [2023-11-14; online 2023-11-14]
DOI Crossref
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
- - (-) - [2023-09-20; online 2023-09-20]
PubMed DOI Crossref
Structural insights into opposing actions of neurosteroids on GABAA receptors.
Legesse DH, Fan C, Teng J, ..., Lindahl E, Hibbs RE
Nat Commun 14 (1) 5091 [2023-08-22; online 2023-08-22]
PubMed DOI Crossref
Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.
Blau C, Yvonnesdotter L, Lindahl E
PLoS Comput Biol 19 (7) e1011255 [2023-07-00; online 2023-07-31]
DOI Crossref
Structure and dynamics of differential ligand binding in the human ρ-type GABA A receptor
Cowgill J, Fan C, Haloi N, ..., Howard RJ, Lindahl E
- - (-) - [2023-06-17; online 2023-06-17]
DOI Crossref
Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
Bergh C, Rovšnik U, Howard RJ, Lindahl E
- - (-) - [2023-04-25; online 2023-04-25]
DOI Crossref
Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM
Bergh C, Rovšnik U, Howard RJ, Lindahl E
- - (-) - [2023-01-06; online 2023-01-06]
PubMed DOI Crossref
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel.
Lycksell M, Rovšnik U, Hanke A, ..., Howard RJ, Lindahl E
Proc. Natl. Acad. Sci. U.S.A. 119 (50) e2210669119 [2022-12-13; online 2022-12-08]
DOI Crossref
Automated simulation-based membrane-protein refinement into cryo-EM data
Yvonnesdotter L, Rovšnik U, Blau C, ..., Howard RJ, Lindahl E
- - (-) - [2022-10-31; online 2022-10-31]
PubMed DOI Crossref
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators.
Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E
Proc. Natl. Acad. Sci. U.S.A. 119 (43) e2208081119 [2022-10-25; online 2022-10-17]
PubMed DOI Crossref
Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium.
Mehregan A, Pérez-Conesa S, Zhuang Y, ..., Ulens C, Delemotte L
Biochim Biophys Acta Biomembr 1864 (10) 183994 [2022-10-01; online 2022-06-18]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities.
Zhu S, Sridhar A, Teng J, ..., Lindahl E, Hibbs RE
Nat Commun 13 (1) 4582 [2022-08-06; online 2022-08-06]
DOI Crossref
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
Lycksell M, Rovšnik U, Hanke A, ..., Howard RJ, Lindahl E
- - (-) - [2022-05-06; online 2022-05-06]
DOI Crossref
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators
Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E
- - (-) - [2022-04-08; online 2022-04-08]
DOI Crossref
Predictions of Skin Permeability Using Molecular Dynamics Simulation from Two-Dimensional Sampling of Spatial and Alchemical Perturbation Reaction Coordinates
Lundborg M, Wennberg C, Lidmar J, ..., Lindahl E, Norlén L
- - (-) - [2022-02-10; online 2022-02-10]
PubMed DOI Crossref
Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel.
Bergh C, Heusser SA, Howard R, Lindahl E
Elife 10 (-) - [2021-10-15; online 2021-10-15]
DOI Crossref
Author response: Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel
Bergh C, Heusser SA, Howard R, Lindahl E
- - (-) - [2021-10-01; online 2021-10-01]
PubMed DOI Crossref
Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations.
Rovšnik U, Zhuang Y, Forsberg BO, ..., Howard RJ, Lindahl E
Life Sci. Alliance 4 (8) - [2021-08-00; online 2021-07-01]
DOI Crossref
Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering
Lycksell M, Rovšnik U, Bergh C, ..., Howard RJ, Lindahl E
- - (-) - [2021-04-11; online 2021-04-11]
PubMed DOI Crossref
Bacterial protein domains with a novel Ig-like fold target human CEACAM receptors.
van Sorge NM, Bonsor DA, Deng L, ..., Lindahl G, McCarthy AJ
EMBO J. 40 (7) e106103 [2021-04-01; online 2021-02-01]
DOI Crossref
A cationic lipid site at the outward transmembrane face of a pentameric ligand-gated ion channel
Sridhar A, Lummis SCR, Pasini D, ..., Howard RJ, Ulens C
- - (-) - [2021-03-25; online 2021-03-25]
DOI Crossref
Markov State Models of Proton- and Gate-Dependent Activation in a Pentameric Ligand-Gated Ion Channel
Bergh C, Heusser SA, Howard RJ, Lindahl E
- - (-) - [2021-03-12; online 2021-03-12]
DOI Crossref
Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations
Rovšnik U, Zhuang Y, Forsberg BO, ..., Howard RJ, Lindahl E
- - (-) - [2021-01-05; online 2021-01-05]
DOI Crossref
A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics
Gossen J, Albani S, Hanke A, ..., Kokh DB, Rossetti G
- - (-) - [2020-12-15; online 2020-12-15]
PubMed DOI Crossref
Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS.
Páll S, Zhmurov A, Bauer P, ..., Hess B, Lindahl E
J Chem Phys 153 (13) 134110 [2020-10-07; online 2020-10-10]
DOI Crossref
Assembly and symmetry of the fungal E3BP-containing core of the Pyruvate Dehydrogenase Complex
Forsberg BO, Aibara S, Howard RJ, Mortezaei N, Lindahl E
- - (-) - [2020-08-14; online 2020-08-14]
DOI Crossref
Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations
Rovšnik U, Zhuang Y, Axelsson L, ..., Howard R, Lindahl E
- - (-) - [2020-06-20; online 2020-06-20]
DOI Crossref
Bacterial protein domains with a novel Ig-like fold target human CEACAM receptors
van Sorge NM, Bonsor DA, Deng L, ..., Lindahl G, McCarthy AJ
- - (-) - [2020-06-10; online 2020-06-10]
DOI Crossref
Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA
Madru C, Raia P, Hugonneau-Beaufet I, ..., Carroni M, Sauguet L
- - (-) - [2020-01-30; online 2020-01-30]
PubMed DOI Crossref
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.
Elofsson A, Hess B, Lindahl E, ..., van der Spoel D, Wallqvist A
PLoS Comput Biol 15 (1) e1006649 [2019-01-00; online 2019-01-17]
PubMed DOI Crossref
New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Zivanov J, Nakane T, Forsberg BO, ..., Lindahl E, Scheres SH
Elife 7 (-) - [2018-11-09; online 2018-11-09]
DOI Crossref
Author response: New tools for automated high-resolution cryo-EM structure determination in RELION-3
Zivanov J, Nakane T, Forsberg BO, ..., Lindahl E, Scheres SH
- - (-) - [2018-11-05; online 2018-11-05]
DOI Crossref
RELION-3: new tools for automated high-resolution cryo-EM structure determination
Zivanov J, Nakane T, Forsberg B, ..., Lindahl E, Scheres SHW
- - (-) - [2018-09-19; online 2018-09-19]
PubMed DOI Crossref
Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.
Nakane T, Kimanius D, Lindahl E, Scheres SH
Elife 7 (-) - [2018-06-01; online 2018-06-01]
DOI Crossref
Author response: Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
Nakane T, Kimanius D, Lindahl E, Scheres SH
- - (-) - [2018-05-10; online 2018-05-10]
DOI Crossref
Molecular basis for voltage sensitivity in membrane proteins
Kasimova MA, Lindahl E, Delemotte L
- - (-) - [2018-04-05; online 2018-04-05]
PubMed DOI Crossref
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.
Kimanius D, Forsberg BO, Scheres SH, Lindahl E
Elife 5 (-) - [2016-11-15; online 2016-11-15]
DOI Crossref
Author response: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
Kimanius D, Forsberg BO, Scheres SH, Lindahl E
- - (-) - [2016-10-16; online 2016-10-16]
SciLifeLab Data Centre
Publications 9.5.1