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Erik Lindahl - Publications

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Year Citation  Score
2024 Bergh C, Rovšnik U, Howard R, Lindahl E. Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. Elife. 12. PMID 38289224 DOI: 10.7554/eLife.86016  0.333
2021 Rovšnik U, Zhuang Y, Forsberg BO, Carroni M, Yvonnesdotter L, Howard RJ, Lindahl E. Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations. Life Science Alliance. 4. PMID 34210687 DOI: 10.26508/lsa.202101011  0.309
2020 Forsberg BO, Aibara S, Howard RJ, Mortezaei N, Lindahl E. Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex. Nature Communications. 11: 4667. PMID 32938938 DOI: 10.1038/S41467-020-18401-Z  0.307
2020 Kim JJ, Gharpure A, Teng J, Zhuang Y, Howard RJ, Zhu S, Noviello CM, Walsh RM, Lindahl E, Hibbs RE. Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature. PMID 32879488 DOI: 10.1038/S41586-020-2654-5  0.321
2020 Grottesi A, Bešker N, Emerson A, Manelfi C, Beccari AR, Frigerio F, Lindahl E, Cerchia C, Talarico C. Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations. International Journal of Molecular Sciences. 21. PMID 32731361 DOI: 10.3390/Ijms21155346  0.318
2020 Hu H, Howard RJ, Bastolla U, Lindahl E, Delarue M. Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 32482881 DOI: 10.1073/Pnas.1922701117  0.417
2020 Howard RJ, Zhuang Y, Heusser SA, Bergh CC, Rovsnik U, Orellana L, Lindahl E. Allosteric Gating Determinants in the Transmembrane Domain of Pentameric Ligand-Gated Ion Channels Biophysical Journal. 118: 584a. DOI: 10.1016/J.Bpj.2019.11.3169  0.37
2020 Rovsnik U, Lim V, Blau C, Howard RJ, Lindahl E. Cryo-EM Structure Determination and Model Fitting of the Proton-Gated Ligand-Gated Ion Channel glic at Multiple pH States Biophysical Journal. 118: 581a-582a. DOI: 10.1016/J.Bpj.2019.11.3155  0.375
2020 Bergh C, Orellana L, Heusser SA, Howard RJ, Lindahl E. Mapping pH-Dependent State Transitions of a Pentameric Ligand-gated Ion Channel through Markov State Modeling Biophysical Journal. 118: 191a. DOI: 10.1016/J.Bpj.2019.11.1160  0.328
2019 Gharpure A, Teng J, Zhuang Y, Noviello CM, Walsh RM, Cabuco R, Howard RJ, Zaveri NT, Lindahl E, Hibbs RE. Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor. Neuron. PMID 31488329 DOI: 10.1016/J.Bpj.2019.11.3177  0.331
2019 Orellana L, Thorne AH, Lema R, Gustavsson J, Parisian AD, Hospital A, Cordeiro TN, Bernadó P, Scott AM, Brun-Heath I, Lindahl E, Cavenee WK, Furnari FB, Orozco M. Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope. Proceedings of the National Academy of Sciences of the United States of America. PMID 31028138 DOI: 10.1073/Pnas.1821442116  0.315
2019 Wang K, Preisler SS, Zhang L, Cui Y, Missel JW, Grønberg C, Gotfryd K, Lindahl E, Andersson M, Calloe K, Egea PF, Klaerke DA, Pusch M, Pedersen PA, Zhou ZH, et al. Structure of the human ClC-1 chloride channel. Plos Biology. 17: e3000218. PMID 31022181 DOI: 10.1371/Journal.Pbio.3000218  0.387
2019 Orellana L, Gustavsson J, Bergh C, Yoluk O, Lindahl E. eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. Bioinformatics (Oxford, England). PMID 30838394 DOI: 10.1093/Bioinformatics/Btz104  0.311
2019 Rovsnik U, Howard R, Forsberg B, Carroni M, Lindahl E. Characterizing Functional States of a Model Ligand-Gated Ion Channel by Cryo-Electron Microscopy Biophysical Journal. 116: 160a. DOI: 10.1016/J.Bpj.2018.11.885  0.356
2019 Lycksell M, Johansen NT, Howard RJ, Arleth L, Lindahl E. Probing Structural States of a Pentameric Ligand-Gated Ion Channel with Small Angle Neutron Scattering Biophysical Journal. 116: 36a-37a. DOI: 10.1016/J.Bpj.2018.11.241  0.358
2019 Delarue MH, Hu H, Howard RJ, Rovsnik U, Hlioui S, Lindahl E. Structural Studies of the Gating Mechanism in a Pentameric Ligand-Gated Ion Channel Containing Two Additional N-Terminal Periplasmic Domains Biophysical Journal. 116: 396a. DOI: 10.1016/J.Bpj.2018.11.2140  0.379
2019 Bergh CC, Orellana L, Howard RJ, Lindahl E. Understanding the Conformational Dynamics of a Pentameric Ligand-Gated Ion Channel through Markov State Modeling Biophysical Journal. 116: 395a-396a. DOI: 10.1016/J.Bpj.2018.11.2138  0.393
2019 Howard RJ, Zhuang Y, Nakamura S, Lycksell M, Kiik H, Rovšnik U, Bergh C, Heusser SA, Orellana L, Lindahl E. Allosteric Modulation via Transmembrane Interfaces in a Pentameric Ligand-Gated Ion Channel Biophysical Journal. 116: 245a-246a. DOI: 10.1016/J.Bpj.2018.11.1344  0.369
2018 Heusser SA, Lycksell M, Wang X, McComas SE, Howard RJ, Lindahl E. Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity. Proceedings of the National Academy of Sciences of the United States of America. PMID 30275330 DOI: 10.1016/J.Bpj.2018.11.2137  0.426
2018 Kimanius D, Lindahl E, Andersson M. Uptake dynamics in the Lactose permease (LacY) membrane protein transporter. Scientific Reports. 8: 14324. PMID 30254312 DOI: 10.1038/S41598-018-32624-7  0.342
2018 Kasimova MA, Lindahl E, Delemotte L. Determining the molecular basis of voltage sensitivity in membrane proteins. The Journal of General Physiology. PMID 30150239 DOI: 10.1085/Jgp.201812086  0.339
2018 Perez Boerema A, Aibara S, Paul B, Tobiasson V, Kimanius D, Forsberg BO, Wallden K, Lindahl E, Amunts A. Publisher Correction: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor. Nature Plants. PMID 30038411 DOI: 10.1038/S41477-018-0203-0  0.607
2018 Lundborg M, Narangifard A, Wennberg CL, Lindahl E, Daneholt B, Norlén L. Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation. Journal of Structural Biology. PMID 29702212 DOI: 10.1016/J.Jsb.2018.04.005  0.335
2018 Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Reports. 23: 993-1004. PMID 29694907 DOI: 10.1016/J.Celrep.2018.03.108  0.421
2018 Boerema AP, Aibara S, Paul B, Tobiasson V, Kimanius D, Forsberg BO, Wallden K, Lindahl E, Amunts A. Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor. Nature Plants. 4: 212-217. PMID 29610536 DOI: 10.2210/Pdb6Eri/Pdb  0.654
2018 Wennberg CL, Narangifard A, Lundborg M, Norlén L, Lindahl E. Structural Transitions in Ceramide Cubic Phases during Formation of the Human Skin Barrier. Biophysical Journal. 114: 1116-1127. PMID 29539398 DOI: 10.1016/J.Bpj.2017.12.039  0.3
2018 Howard RJ, Heusser SA, Zhuang Y, Lycksell M, Klement G, Orellana L, Lindahl E. Alcohol Modulation Via Allosteric Transmembrane Sites In Pentameric Ligand-Gated Ion Channels Alcoholism: Clinical and Experimental Research. 42. DOI: 10.1111/Acer.13834  0.348
2018 Heusser SA, Lycksell M, Wang X, Howard RJ, Lindahl E. Flexibility of a Transmembrane Helix Underlies Dramatic Reversal of Net Anesthetic Effects in a Pentameric Ligand-Gated Ion Channel Biophysical Journal. 114: 488a-489a. DOI: 10.1016/J.Bpj.2017.11.2680  0.383
2018 Lycksell M, Heusser SA, Howard RJ, Lindahl E. Expansion of a Transmembrane Cavity Facilitates Anesthetic Potentiation of a Pentameric Ligand Gated Ion Channel Biophysical Journal. 114: 299a. DOI: 10.1016/J.Bpj.2017.11.1707  0.37
2018 Howard RJ, Fourati Z, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Details of an Allosteric Mechanism for Bimodal Anesthetic Modulation of Pentameric Ligand-Gated Ion Channels Biophysical Journal. 114: 204a. DOI: 10.1016/J.Bpj.2017.11.1137  0.392
2017 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. Iucrj. 4: 723-727. PMID 29123673 DOI: 10.1107/S205225251701226X  0.617
2017 Ottosson NE, Silverå Ejneby M, Wu X, Yazdi S, Konradsson P, Lindahl E, Elinder F. A drug pocket at the lipid bilayer-potassium channel interface. Science Advances. 3: e1701099. PMID 29075666 DOI: 10.1126/Sciadv.1701099  0.384
2017 Kimanius D, White S, Lindahl E, Kaback R, Andersson M. Uptake Dynamics in the LacY Membrane Protein Transporter Biophysical Journal. 112: 128a. DOI: 10.1016/J.Bpj.2016.11.715  0.355
2017 Heusser SA, Howard RJ, Fourati Z, Delarue M, Lindahl E. Structural and Functional Evidence for Multi-Site Allostery Mediated by General Anesthetics in a Model Ligand-Gated Ion Channel Biophysical Journal. 112: 554a. DOI: 10.1016/J.Bpj.2016.11.2990  0.42
2017 Howard RJ, Heusser SA, Yoluk Ö, Snow O, Klement G, Mola AR, MD Ruel T, Lindahl E. Transmembrane Structural Determinants of Alcohol Binding and Modulation in a Model Ligand-Gated Ion Channel Biophysical Journal. 112: 554a. DOI: 10.1016/J.Bpj.2016.11.2988  0.379
2017 Ottosson N, Silverå Ejneby M, Wu X, Yazdi S, Konradsson P, Lindahl E, Elinder F. Drug Interaction at the Lipid Bilayer-Potassium Channel Interface Biophysical Journal. 112: 40a. DOI: 10.1016/J.Bpj.2016.11.253  0.378
2016 Grønberg C, Sitsel O, Lindahl E, Gourdon P, Andersson M. Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport. Biophysical Journal. 111: 2417-2429. PMID 27926843 DOI: 10.1016/J.Bpj.2016.10.020  0.335
2016 Kimanius D, Forsberg BO, Scheres SH, Lindahl E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Elife. 5. PMID 27845625 DOI: 10.7554/Elife.18722  0.315
2016 Nys M, Wijckmans E, Farinha A, Yoluk Ö, Andersson M, Brams M, Spurny R, Peigneur S, Tytgat J, Lindahl E, Ulens C. Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine. Proceedings of the National Academy of Sciences of the United States of America. 113: E6696-E6703. PMID 27791038 DOI: 10.1073/Pnas.1603101113  0.381
2016 Öjemalm K, Higuchi T, Lara P, Lindahl E, Suga H, von Heijne G. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids. Proceedings of the National Academy of Sciences of the United States of America. PMID 27601675 DOI: 10.1073/Pnas.1606776113  0.302
2016 Orellana L, Yoluk O, Carrillo O, Orozco M, Lindahl E. Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations. Nature Communications. 7: 12575. PMID 27578633 DOI: 10.1038/Ncomms12575  0.359
2016 Conti L, Renhorn J, Gabrielsson A, Turesson F, Liin SI, Lindahl E, Elinder F. Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation. Scientific Reports. 6: 27562. PMID 27278891 DOI: 10.1038/Srep27562  0.344
2016 Heusser SA, Yoluk Ö, Klement G, Riederer EA, Lindahl E, Howard RJ. Functional characterization of neurotransmitter activation and modulation in a nematode model ligand-gated ion channel. Journal of Neurochemistry. PMID 27102368 DOI: 10.1111/Jnc.13644  0.427
2016 Yazdi S, Stein M, Elinder F, Andersson M, Lindahl E. The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. Plos Computational Biology. 12: e1004704. PMID 26751683 DOI: 10.1371/Journal.Pcbi.1004704  0.402
2016 Forsberg BO, Kimanius D, Lindahl E. Higher Resolution with the Same Data - Tuning cryo-EM Refinement in Relion Biophysical Journal. 110: 157a. DOI: 10.1016/J.Bpj.2015.11.880  0.302
2016 Blau C, Lenner N, Kutzner C, Grubmuller H, Lindahl E. From CRYO-EM Densities to Atom Coordinates and Ensembles with Bayes Approach Biophysical Journal. 110: 156a-157a. DOI: 10.1016/J.Bpj.2015.11.878  0.329
2016 Liin S, Gabrielsson A, Elinder F, Lindahl E. The Molecular Mechanism of the Dual Spider Toxin Effect on Voltage Gated K+ Channels Biophysical Journal. 110: 107a. DOI: 10.1016/J.Bpj.2015.11.632  0.373
2016 Conti L, Renhorn J, Gabrielsson A, Turesson F, Liin S, Lindahl E, Elinder F. A Reciprocal Voltage Sensor-To-Pore Coupling in C-Type Inactivation Biophysical Journal. 110: 104a. DOI: 10.1016/J.Bpj.2015.11.620  0.328
2016 Orellana L, Yoluk O, Orozco M, Lindahl E. Revealing the Mechanism for Conformational Changes from Structurally Rich Ensembles Biophysical Journal. 110: 54a. DOI: 10.1016/J.Bpj.2015.11.358  0.395
2016 Yoluk O, Orellana L, Bertaccini EJ, Trudell JR, Lindahl E. Principal Components from Ligand-Gated Ion Channel Structures Enable Ensemble Studies of Microsecond-Scale Transitions Biophysical Journal. 110: 454. DOI: 10.1016/J.Bpj.2015.11.2433  0.38
2015 Wennberg CL, Murtola T, Páll S, Abraham MJ, Hess B, Lindahl E. Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation. Journal of Chemical Theory and Computation. 11: 5737-46. PMID 26587968 DOI: 10.1021/Acs.Jctc.5B00726  0.301
2015 Kimanius D, Pettersson I, Schluckebier G, Lindahl E, Andersson M. SAXS-Guided Metadynamics. Journal of Chemical Theory and Computation. 11: 3491-8. PMID 26575782 DOI: 10.1021/Acs.Jctc.5B00299  0.332
2015 Yoluk Ö, Lindahl E, Andersson M. Conformational gating dynamics in the GluCl anion-selective chloride channel. Acs Chemical Neuroscience. 6: 1459-67. PMID 25992588 DOI: 10.1021/Acschemneuro.5B00111  0.423
2015 Voigt TB, Heusser S, Klement G, Pouya, I, Mola AR, Ruel TMD, Trudell JR, Lindahl E, Howard RJ. P-54PHYSICOCHEMICAL DETERMINANTS OF ALCOHOL BINDING IN A MODEL LIGAND-GATED ION CHANNEL Alcohol and Alcoholism. 50: i59.1-i59. DOI: 10.1093/Alcalc/Agv080.54  0.387
2015 Heusser SA, Yoluk O, Lindahl E. Exploring the Gating Pathway in an Eukaryotic Ligand-Gated Ion Channel Biophysical Journal. 108: 433a. DOI: 10.1016/J.Bpj.2014.11.2365  0.41
2015 Yoluk Ö, Heusser S, Pouya I, Howard R, Klement G, Lindahl E. Opening and Selectivity of the Glic Ligand-Gated Ion Channel can be Tuned by Mutation of Hydrophobic Residues in the Pore Biophysical Journal. 108: 431a. DOI: 10.1016/J.Bpj.2014.11.2357  0.363
2015 Yoluk O, Heusser S, Andersson M, Orellana L, Lindahl E. Gating Ritual: Simulations of Gating in Glutamate-Gated Chloride Channel Biophysical Journal. 108: 431a. DOI: 10.1016/J.Bpj.2014.11.2355  0.428
2015 Andersson M, Lindahl E, White SH, Kaback RH. The Molecular Basis for Substrate Specificity in Lactose Permease Biophysical Journal. 108: 309a. DOI: 10.1016/J.Bpj.2014.11.1680  0.369
2014 Lundborg M, Apostolov R, Spångberg D, Gärdenäs A, van der Spoel D, Lindahl E. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry. 35: 260-9. PMID 24258850 DOI: 10.1002/Jcc.23495  0.312
2014 Olsen RW, Li GD, Wallner M, Trudell JR, Bertaccini EJ, Lindahl E, Miller KW, Alkana RL, Davies DL. Structural models of ligand-gated ion channels: sites of action for anesthetics and ethanol. Alcoholism, Clinical and Experimental Research. 38: 595-603. PMID 24164436 DOI: 10.1111/Acer.12283  0.409
2014 Yazdi S, Andersson M, Elinder F, Stein M, Lindahl E. Molecular Characterization of the Binding of Polyunsaturated Fatty Acids to a Voltage-Gated Potassium Channel Biophysical Journal. 106: 739a. DOI: 10.1016/J.Bpj.2013.11.4071  0.341
2014 Gabrielsson A, Liin S, Elinder F, Lindahl E. Binding Structure & Dynamics for Toxins Modifying the Gating Mechanism of Kv Channels Biophysical Journal. 106: 738a. DOI: 10.1016/J.Bpj.2013.11.4066  0.44
2014 Yoluk O, Riederer EA, Andersson M, Klement G, Trudell JR, Bertaccini EJ, Howard RJ, Lindahl E. Contribution of Structural Elements to Activation and Allosteric Modulation in an Anionic Ligand-Gated Ion Channel Biophysical Journal. 106: 547a. DOI: 10.1016/J.Bpj.2013.11.3046  0.375
2014 Riederer E, Yoluk O, Trudell J, Lindahl E, Harris A, Howard R. Alcohol Modulation of a Eukaryotic Ligand-Gated Ion Channel of Known Structure Biophysical Journal. 106: 545a. DOI: 10.1016/J.Bpj.2013.11.3034  0.337
2014 Pouya I, Klement G, Murail S, Kasson P, Yoluk Ö, Lindahl E. Altering the Open vs. Closed State Balance of the GLIC Ligand-Gated Ion Channel through Mutagenesis Enables Molecular Simulation of the Reversible Gating Process Biophysical Journal. 106: 343a. DOI: 10.1016/J.Bpj.2013.11.1959  0.455
2014 Klement G, Pouya I, Yoluk Ö, Howard R, Lindahl E. Ligand-Gated Ion Channel Gating Kinetics and the Opening/Closing Mechanism are Sensitive to Mutations Altering the Hydrophobicity of the Ion Conduction Pore Biophysical Journal. 106: 343a. DOI: 10.1016/J.Bpj.2013.11.1958  0.405
2014 Arrar M, Pouya I, McCammon JA, Lindahl E. Molecular Insights into the Gating Mechanism of GLIC, a Prokaryotic Ligand-Gated Ion Channel Biophysical Journal. 106: 342a. DOI: 10.1016/J.Bpj.2013.11.1957  0.412
2014 Larsson P, Pouya I, Lindahl E. From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding Israel Journal of Chemistry. 54: 1274-1285. DOI: 10.1002/Ijch.201400020  0.318
2013 Wennberg CL, Murtola T, Hess B, Lindahl E. Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties. Journal of Chemical Theory and Computation. 9: 3527-37. PMID 26584109 DOI: 10.1021/Ct400140N  0.33
2013 Santacruz-Perez C, Pegos VR, Honorato RV, Verli H, Lindahl E, Barbosa JA, Balan A. A specific interdomain interaction preserves the structural and binding properties of the ModA protein from the phytopathogen Xanthomonas citri domain interaction and transport in ModA. Archives of Biochemistry and Biophysics. 539: 20-30. PMID 24035743 DOI: 10.1016/J.Abb.2013.09.003  0.371
2013 Heusser SA, Howard RJ, Borghese CM, Cullins MA, Broemstrup T, Lee US, Lindahl E, Carlsson J, Harris RA. Functional validation of virtual screening for novel agents with general anesthetic action at ligand-gated ion channels. Molecular Pharmacology. 84: 670-8. PMID 23950219 DOI: 10.1124/Mol.113.087692  0.342
2013 Yoluk O, Brömstrup T, Bertaccini EJ, Trudell JR, Lindahl E. Stabilization of the GluCl ligand-gated ion channel in the presence and absence of ivermectin. Biophysical Journal. 105: 640-7. PMID 23931312 DOI: 10.1016/J.Bpj.2013.06.037  0.436
2013 Brömstrup T, Howard RJ, Trudell JR, Harris RA, Lindahl E. Inhibition versus potentiation of ligand-gated ion channels can be altered by a single mutation that moves ligands between intra- and intersubunit sites. Structure (London, England : 1993). 21: 1307-16. PMID 23891290 DOI: 10.1016/J.Str.2013.06.018  0.342
2013 Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England). 29: 845-54. PMID 23407358 DOI: 10.1093/Bioinformatics/Btt055  0.348
2013 Schwaiger CS, Liin SI, Elinder F, Lindahl E. The conserved phenylalanine in the K+ channel voltage-sensor domain creates a barrier with unidirectional effects. Biophysical Journal. 104: 75-84. PMID 23332060 DOI: 10.1016/J.Bpj.2012.11.3827  0.369
2013 Kasson PM, Hess B, Lindahl E. Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions. Chemistry and Physics of Lipids. 169: 106-12. PMID 23318532 DOI: 10.1016/J.Chemphyslip.2013.01.001  0.352
2013 Paulsen PA, Jurkowski W, Apostolov R, Lindahl E, Nissen P, Poulsen H. The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology. Molecular Membrane Biology. 30: 195-205. PMID 22913437 DOI: 10.3109/09687688.2012.713520  0.302
2013 Henrion U, Schwaiger CS, Börjesson SI, Elinder F, Lindahl E. Tracking a Voltage-Sensor Cycle with Models of Intermediate States from Metal-Ion Bridge Constraints Biophysical Journal. 104: 124a-125a. DOI: 10.1016/J.Bpj.2012.11.717  0.393
2013 Kasson PM, Lindahl E. Local Stresses in Fusing Membranes from Molecular Simulation Biophysical Journal. 104: 92a. DOI: 10.1016/J.Bpj.2012.11.549  0.308
2013 Yoluk O, Andersson M, Lindahl E. Improved Comparative Models of Human Gabaar Ligand-Gated Ion Channels Based on Structural Dynamics of GluCl Biophysical Journal. 104: 638a. DOI: 10.1016/J.Bpj.2012.11.3521  0.395
2013 Howard RJ, Sauguet L, Broemstrup T, Murail S, Lee US, Horani S, Trudell JR, Corringer P, Lindahl E, Delarue M, Harris RA. Alcohol and Anesthetic Binding to Pentameric Ligand-Gated Ion Channels Revealed in a Prokaryotic Model System Biophysical Journal. 104: 635a-636a. DOI: 10.1016/J.Bpj.2012.11.3512  0.355
2013 Pouya I, Pronk S, Rotskoff G, Kasson PM, Lindahl E. Ligand-Gated Ion Channel Opening and Closing Mechanism from Molecular Simulations Biophysical Journal. 104: 271a. DOI: 10.1016/J.Bpj.2012.11.1518  0.435
2012 Lindahl E. Unraveling the strokes of ion channel molecular machines in computers. Proceedings of the National Academy of Sciences of the United States of America. 109: 21186-7. PMID 23236147 DOI: 10.1073/Pnas.1218763110  0.368
2012 Vargas E, Yarov-Yarovoy V, Khalili-Araghi F, Catterall WA, Klein ML, Tarek M, Lindahl E, Schulten K, Perozo E, Bezanilla F, Roux B. An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. The Journal of General Physiology. 140: 587-94. PMID 23183694 DOI: 10.1085/Jgp.201210873  0.416
2012 Schwaiger CS, Börjesson SI, Hess B, Wallner B, Elinder F, Lindahl E. The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain. Plos One. 7: e45880. PMID 23094020 DOI: 10.1371/Journal.Pone.0045880  0.365
2012 Murail S, Howard RJ, Broemstrup T, Bertaccini EJ, Harris RA, Trudell JR, Lindahl E. Molecular mechanism for the dual alcohol modulation of Cys-loop receptors. Plos Computational Biology. 8: e1002710. PMID 23055913 DOI: 10.1371/Journal.Pcbi.1002710  0.315
2012 Henrion U, Renhorn J, Börjesson SI, Nelson EM, Schwaiger CS, Bjelkmar P, Wallner B, Lindahl E, Elinder F. Tracking a complete voltage-sensor cycle with metal-ion bridges. Proceedings of the National Academy of Sciences of the United States of America. 109: 8552-7. PMID 22538811 DOI: 10.1073/Pnas.1116938109  0.399
2012 Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CW, Johnson AP, Madge D, Lindahl E, Rolland JF, de Groot BL. Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp. Chemmedchem. 7: 1775-83. PMID 22473914 DOI: 10.1002/Cmdc.201100600  0.321
2012 Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature. 481: 525-9. PMID 22230960 DOI: 10.1038/Nature10742  0.345
2012 Murail S, Howard RJ, Trudell JR, Bertaccini E, Lindahl E. Tracing the Closing of a Ligand-Gated Ion Channel in Atomic Detail: An Unconstrained Four-Microsecond Simulation of GLIC Leads to a Closed State Remarkably Similar to ELIC Biophysical Journal. 102: 113a-114a. DOI: 10.1016/J.Bpj.2011.11.639  0.389
2012 Yoluk O, Murail S, Lindahl E. Simulations of Subunit Interactions in the C. Elegans GluCl Ligand-Gated Ion Channel Biophysical Journal. 102: 472a. DOI: 10.1016/J.Bpj.2011.11.2587  0.398
2012 Schwaiger CS, Börjesson SI, Hess B, Elinder F, Lindahl E. Phe233 in the Voltage-Sensor is Rate Limiting for Channel Closure but not for the Opening Biophysical Journal. 102: 13a. DOI: 10.1016/J.Bpj.2011.11.096  0.393
2011 Howard RJ, Murail S, Ondricek KE, Corringer PJ, Lindahl E, Trudell JR, Harris RA. Structural basis for alcohol modulation of a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America. 108: 12149-54. PMID 21730162 DOI: 10.1073/Pnas.1104480108  0.33
2011 Murail S, Wallner B, Trudell JR, Bertaccini E, Lindahl E. Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor. Biophysical Journal. 100: 1642-50. PMID 21463577 DOI: 10.1016/J.Bpj.2011.02.032  0.375
2011 Schwaiger CS, Bjelkmar P, Hess B, Lindahl E. 3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state. Biophysical Journal. 100: 1446-54. PMID 21402026 DOI: 10.1016/J.Bpj.2011.02.003  0.335
2011 Kasson PM, Lindahl E, Pande VS. Water ordering at membrane interfaces controls fusion dynamics. Journal of the American Chemical Society. 133: 3812-5. PMID 21351772 DOI: 10.1021/Ja200310D  0.32
2011 Larsson P, Hess B, Lindahl E. Algorithm improvements for molecular dynamics simulations Wiley Interdisciplinary Reviews: Computational Molecular Science. 1: 93-108. DOI: 10.1002/Wcms.3  0.312
2010 Bjelkmar P, Larsson P, Cuendet MA, Hess B, Lindahl E. Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. Journal of Chemical Theory and Computation. 6: 459-66. PMID 26617301 DOI: 10.1021/Ct900549R  0.323
2010 Bertaccini EJ, Trudell JR, Lindahl E. Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model. Acs Chemical Neuroscience. 1: 552-8. PMID 22816018 DOI: 10.1021/Cn100026T  0.386
2010 Bertaccini EJ, Wallner B, Trudell JR, Lindahl E. Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM4. Journal of Chemical Information and Modeling. 50: 2248-55. PMID 21117677 DOI: 10.1021/Ci100266C  0.411
2010 Ray A, Lindahl E, Wallner B. Model quality assessment for membrane proteins. Bioinformatics (Oxford, England). 26: 3067-74. PMID 20947525 DOI: 10.1093/Bioinformatics/Btq581  0.329
2010 Larsson P, Lindahl E. A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescaling. Journal of Computational Chemistry. 31: 2593-600. PMID 20740558 DOI: 10.1002/Jcc.21552  0.325
2010 Kasson PM, Lindahl E, Pande VS. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. Plos Computational Biology. 6: e1000829. PMID 20585620 DOI: 10.1371/Journal.Pcbi.1000829  0.342
2010 Niemelä PS, Miettinen MS, Monticelli L, Hammaren H, Bjelkmar P, Murtola T, Lindahl E, Vattulainen I. Membrane proteins diffuse as dynamic complexes with lipids. Journal of the American Chemical Society. 132: 7574-5. PMID 20469857 DOI: 10.1021/Ja101481B  0.307
2010 Murail S, Wallner B, Trudell JR, Bertaccini E, Lindahl E. Microsecond Simulations Show that Ethanol Binds between Subunits and Stabilizes the Open Form of a Glycine Receptor Model Biophysical Journal. 98: 704a-705a. DOI: 10.1016/J.Bpj.2009.12.3865  0.38
2010 Kasson P, Lindahl E, Pande V. Atomic-Resolution Simulations Yield New Insight into Vesicle Fusion and Fusion Protein Mechanisms Biophysical Journal. 98: 616a. DOI: 10.1016/J.Bpj.2009.12.3363  0.34
2010 Schwaiger CS, Bjelkmar P, Hess B, Lindahl E. Structural Transition from Alpha- to 3_10-Helix Reduces the Free Energy Required for S4 Translation in Kv1.2/2.1 Voltage Sensors, and F233 Appears to Responsible for the Gating Barrier Biophysical Journal. 98: 520a. DOI: 10.1016/J.Bpj.2009.12.2827  0.372
2010 Lindahl E, Schwaiger C, Bjelkmar P. Microsecond Simulations Indicate 3_10 Helix Transition Facilitates Translation of the S4 Segment of Kv1.2 and Suggest a Hydrophobic Gating Barrier Biophysical Journal. 98: 520a. DOI: 10.1016/J.Bpj.2009.12.2826  0.397
2009 Johansson AC, Lindahl E. Protein contents in biological membranes can explain abnormal solvation of charged and polar residues. Proceedings of the National Academy of Sciences of the United States of America. 106: 15684-9. PMID 19805218 DOI: 10.1073/Pnas.0905394106  0.366
2009 Johansson AC, Lindahl E. The role of lipid composition for insertion and stabilization of amino acids in membranes. The Journal of Chemical Physics. 130: 185101. PMID 19449954 DOI: 10.1063/1.3129863  0.333
2009 Bjelkmar P, Niemelä PS, Vattulainen I, Lindahl E. Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel. Plos Computational Biology. 5: e1000289. PMID 19229308 DOI: 10.1371/Journal.Pcbi.1000289  0.454
2009 Johansson AC, Lindahl E. Titratable amino acid solvation in lipid membranes as a function of protonation state. The Journal of Physical Chemistry. B. 113: 245-53. PMID 19118487 DOI: 10.1021/Jp8048873  0.369
2008 Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation. 4: 435-47. PMID 26620784 DOI: 10.1021/Ct700301Q  0.303
2008 Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A. Prediction of membrane-protein topology from first principles. Proceedings of the National Academy of Sciences of the United States of America. 105: 7177-81. PMID 18477697 DOI: 10.1073/Pnas.0711151105  0.317
2008 Lindahl E, Sansom MS. Membrane proteins: molecular dynamics simulations. Current Opinion in Structural Biology. 18: 425-31. PMID 18406600 DOI: 10.1016/J.Sbi.2008.02.003  0.415
2008 Bertaccini EJ, Lindahl E, Sixma T, Trudell JR. Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein. Journal of Chemical Information and Modeling. 48: 855-60. PMID 18348519 DOI: 10.1021/Ci700456S  0.368
2008 Johansson AC, Lindahl E. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins. 70: 1332-44. PMID 17876818 DOI: 10.1002/Prot.21629  0.359
2007 Bertaccini EJ, Trudell JR, Lindahl E. Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Journal of Chemical Information and Modeling. 47: 1572-9. PMID 17602605 DOI: 10.1021/Ci600566J  0.343
2006 Johansson AC, Lindahl E. Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations. Biophysical Journal. 91: 4450-63. PMID 17012325 DOI: 10.1529/Biophysj.106.092767  0.328
2006 Lindahl E, Azuara C, Koehl P, Delarue M. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Research. 34: W52-6. PMID 16845062 DOI: 10.1093/Nar/Gkl082  0.324
2006 Azuara C, Lindahl E, Koehl P, Orland H, Delarue M. PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Research. 34: W38-42. PMID 16845031 DOI: 10.1093/Nar/Gkl072  0.349
2005 Lindahl E, Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Research. 33: 4496-506. PMID 16087736 DOI: 10.1093/Nar/Gki730  0.318
2004 Rhee YM, Sorin EJ, Jayachandran G, Lindahl E, Pande VS. Simulations of the role of water in the protein-folding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 101: 6456-61. PMID 15090647 DOI: 10.1073/Pnas.0307898101  0.307
2003 Hofsäss C, Lindahl E, Edholm O. Molecular dynamics simulations of phospholipid bilayers with cholesterol. Biophysical Journal. 84: 2192-206. PMID 12668428 DOI: 10.1016/S0006-3495(03)75025-5  0.315
2001 Marrink SJ, Lindahl E, Edholm O, Mark AE. Simulation of the spontaneous aggregation of phospholipids into bilayers [23] Journal of the American Chemical Society. 123: 8638-8639. PMID 11525689 DOI: 10.1021/Ja0159618  0.364
2001 Lindahl E, Edholm O. Molecular dynamics simulation of NMR relaxation rates and slow dynamics in lipid bilayers Journal of Chemical Physics. 115: 4938-4950. DOI: 10.1063/1.1389469  0.321
2001 Lindahl E, Hess B, Spoel Dvd. GROMACS 3.0: a package for molecular simulation and trajectory analysis Journal of Molecular Modeling. 7: 306-317. DOI: 10.1007/S008940100045  0.301
2000 Lindahl E, Edholm O. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophysical Journal. 79: 426-33. PMID 10866968 DOI: 10.1016/S0006-3495(00)76304-1  0.307
2000 Lindahl E, Edholm O. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations The Journal of Chemical Physics. 113: 3882-3893. DOI: 10.1063/1.1287423  0.31
Low-probability matches (unlikely to be authored by this person)
2023 Bondarenko V, Chen Q, Singewald K, Haloi N, Tillman TS, Howard RJ, Lindahl E, Xu Y, Tang P. Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization. Acs Chemical Neuroscience. PMID 36821490 DOI: 10.1021/acschemneuro.2c00783  0.299
2005 Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. Journal of Computational Chemistry. 26: 1701-18. PMID 16211538 DOI: 10.1002/Jcc.20291  0.298
2001 Morfeldt E, Berggård K, Persson J, Drakenberg T, Johnsson E, Lindahl E, Linse S, Lindahl G. Isolated hypervariable regions derived from streptococcal M proteins specifically bind human C4b-binding protein: Implications for antigenic variation Journal of Immunology. 167: 3870-3877. PMID 11564804 DOI: 10.4049/Jimmunol.167.7.3870  0.297
2016 Nys M, Farinha A, Wijckmans E, Brams M, Yoluk Ö, Andersson M, Lindahl E, Ulens C. The Crystal Structure of ELIC in Complex with Chlorpromazine Unexpectedly Unveils an Allosteric Binding Site in the Ligand-Binding Domain Biophysical Journal. 110: 457a. DOI: 10.1016/J.Bpj.2015.11.2448  0.296
2008 Johansson ACV, Lindahl E. Correction to the article “Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations” Proteins: Structure, Function, and Bioinformatics. 70: 1655-1656. DOI: 10.1002/Prot.21916  0.296
2022 Lycksell M, Rovšnik U, Hanke A, Martel A, Howard RJ, Lindahl E. Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America. 119: e2210669119. PMID 36480474 DOI: 10.1073/pnas.2210669119  0.295
2019 Elofsson A, Hess B, Lindahl E, Onufriev A, van der Spoel D, Wallqvist A. Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. Plos Computational Biology. 15: e1006649. PMID 30653494 DOI: 10.1371/Journal.Pcbi.1006649  0.293
2021 Lycksell M, Rovšnik U, Bergh C, Johansen NT, Martel A, Porcar L, Arleth L, Howard RJ, Lindahl E. Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34504004 DOI: 10.1073/pnas.2108006118  0.293
2015 Pronk S, Pouya I, Lundborg M, Rotskoff G, Wesén B, Kasson PM, Lindahl E. Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform. Journal of Chemical Theory and Computation. 11: 2600-8. PMID 26575558 DOI: 10.1021/Acs.Jctc.5B00234  0.292
2012 Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CWG, Johnson AP, Madge D, Lindahl E, Rolland J, de Groot BL. Cover Picture: Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2(3)by High-Throughput Virtual Screening and Automated Patch Clamp (ChemMedChem 10/2012) Chemmedchem. 7: 1693-1693. DOI: 10.1002/Cmdc.201290047  0.292
2016 Kimanius D, Forsberg B, Lindahl E. Orders of Magnitude Faster cryo-EM Refinement with GPUs Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.879  0.291
2010 Hennerdal A, Falk J, Lindahl E, Elofsson A. Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Science : a Publication of the Protein Society. 19: 2305-18. PMID 20882639 DOI: 10.1002/Pro.510  0.291
2018 Narangifard A, Den Hollander L, Wennberg CL, Lundborg M, Lindahl E, Iwai I, Han H, Masich S, Daneholt B, Norlén L. Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation. Experimental Cell Research. PMID 29567114 DOI: 10.1016/J.Yexcr.2018.03.010  0.288
2013 Murugan NA, Apostolov R, Rinkevicius Z, Kongsted J, Lindahl E, Ågren H. Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane. Journal of the American Chemical Society. 135: 13590-7. PMID 23951997 DOI: 10.1021/Ja407326N  0.288
2021 Sridhar A, Lummis SCR, Pasini D, Mehregan A, Brams M, Kambara K, Bertrand D, Lindahl E, Howard RJ, Ulens C. Regulation of a pentameric ligand-gated ion channel by a semi-conserved cationic-lipid binding site. The Journal of Biological Chemistry. 100899. PMID 34157288 DOI: 10.1016/j.jbc.2021.100899  0.288
2018 Nakane T, Kimanius D, Lindahl E, Scheres SH. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. Elife. 7. PMID 29856314 DOI: 10.7554/Elife.36861  0.287
2020 Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nature Communications. 11: 1591. PMID 32221299 DOI: 10.1038/S41467-020-15392-9  0.286
2003 Aman K, Lindahl E, Edholm O, Håkansson P, Westlund PO. Structure and dynamics of interfacial water in an Lalpha phase lipid bilayer from molecular dynamics simulations. Biophysical Journal. 84: 102-15. PMID 12524268 DOI: 10.1016/S0006-3495(03)74835-8  0.285
2018 Kasimova MA, Lindahl E, Delemotte L. Detection of Voltage-Sensing Residues in Membrane Proteins Biophysical Journal. 114: 476a. DOI: 10.1016/J.Bpj.2017.11.2618  0.285
2018 Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E, Scheres SH. Author response: New tools for automated high-resolution cryo-EM structure determination in RELION-3 Elife. DOI: 10.7554/Elife.42166.030  0.284
2003 van der Spoel D, Lindahl E. Brute-Force Molecular Dynamics Simulations of Villin Headpiece:  Comparison with NMR Parameters The Journal of Physical Chemistry B. 107: 11178-11187. DOI: 10.1021/Jp034108N  0.284
2001 Håkansson P, Westlund P, Lindahl E, Edholm O. A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a molecular dynamics simulation of the lipid dynamics Physical Chemistry Chemical Physics. 3: 5311-5319. DOI: 10.1039/B105618M  0.282
2021 Bergh C, Heusser SA, Howard R, Lindahl E. Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel. Elife. 10. PMID 34652272 DOI: 10.7554/eLife.68369  0.282
2017 Orellana L, Yoluk Ö, Carrillo O, Orozco M, Lindahl E. Trapping On-Pathway Intermediates for Large Scale Conformational Changes with Coarse-Grained Simulations Biophysical Journal. 112: 485a. DOI: 10.1016/J.Bpj.2016.11.2625  0.28
2009 Ollila OH, Risselada HJ, Louhivuori M, Lindahl E, Vattulainen I, Marrink SJ. 3D pressure field in lipid membranes and membrane-protein complexes. Physical Review Letters. 102: 078101. PMID 19257715 DOI: 10.1103/Physrevlett.102.078101  0.28
1998 Lindahl E, Edholm O. Solvent diffusion outside macromolecular surfaces Physical Review E. 57: 791-796. DOI: 10.1103/Physreve.57.791  0.28
2018 Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E, Scheres SH. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife. 7. PMID 30412051 DOI: 10.7554/Elife.42166  0.279
2014 Andersson M, Mattle D, Sitsel O, Nielsen AM, Lindahl E, White SH, Nissen P, Gourdon P. Transport Pathway in Cu+ P-Type ATPases Biophysical Journal. 106: 427a. DOI: 10.1016/J.Bpj.2013.11.2406  0.278
2019 Raia P, Carroni M, Henry E, Pehau-Arnaudet G, Brûlé S, Béguin P, Henneke G, Lindahl E, Delarue M, Sauguet L. Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. Plos Biology. 17: e3000122. PMID 30657780 DOI: 10.1371/Journal.Pbio.3000122  0.274
2018 Lundborg M, Wennberg CL, Narangifard A, Lindahl E, Norlén L. Predicting drug permeability through skin using molecular dynamics simulation. Journal of Controlled Release : Official Journal of the Controlled Release Society. 283: 269-279. PMID 29864475 DOI: 10.1016/J.Jconrel.2018.05.026  0.272
2012 Wennberg C, Murtola T, Lindahl E. Lattice Summation of Lennard-Jones Interactions in Bilayer Simulations has Critical Effects on Surface Tension Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.936  0.272
2019 Bowman GR, Lindahl E. Decision letter: The dynamic conformational landscape of the protein methyltransferase SETD8 Elife. DOI: 10.7554/Elife.45403.074  0.27
2016 Kimanius D, Forsberg BO, Scheres SH, Lindahl E. Author response: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 Elife. DOI: 10.7554/Elife.18722.024  0.269
2000 Lindahl E, Elofsson A. Identification of related proteins on family, superfamily and fold level. Journal of Molecular Biology. 295: 613-25. PMID 10623551 DOI: 10.1006/Jmbi.1999.3377  0.269
2012 Ray A, Lindahl E, Wallner B. Improved model quality assessment using ProQ2. Bmc Bioinformatics. 13: 224. PMID 22963006 DOI: 10.1186/1471-2105-13-224  0.268
2019 Jordan EJ, Blau C, Lindahl ER. Combining Cryo-EM and Simulation to Understand Ligand Binding in Pentameric Ligand Gated Ion Channels Biophysical Journal. 116: 569a. DOI: 10.1016/j.bpj.2018.11.3061  0.268
2015 Lundborg M, Lindahl E. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations. The Journal of Physical Chemistry. B. 119: 810-23. PMID 25343332 DOI: 10.1021/Jp505332P  0.266
2014 Pronk S, Lindahl E, Kasson PM. Dynamic heterogeneity controls diffusion and viscosity near biological interfaces. Nature Communications. 5: 3034. PMID 24398864 DOI: 10.1038/Ncomms4034  0.266
2022 Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E. Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators. Proceedings of the National Academy of Sciences of the United States of America. 119: e2208081119. PMID 36251999 DOI: 10.1073/pnas.2208081119  0.265
2019 Wells MM, Bondarenko V, Tillman TS, Singewald K, Lawless MJ, Caporoso J, Brandon N, Chen C, Kinde MN, Saxena S, Xu Y, Lindahl E, Tang P. Integrative Structure Determination of α7nAChR Intracellular Domain Biophysical Journal. 116: 394a. DOI: 10.1016/J.Bpj.2018.11.2133  0.262
2008 Larsson P, Wallner B, Lindahl E, Elofsson A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Science : a Publication of the Protein Society. 17: 990-1002. PMID 18441233 DOI: 10.1110/Ps.073344908  0.257
2019 Gharpure A, Teng J, Zhuang Y, Noviello CM, Walsh RM, Cabuco R, Howard RJ, Zaveri NT, Lindahl E, Hibbs RE. Agonist Selectivity and Ion Permeation in the alpha 3 beta 4 Ganglionic Nicotinic Receptor Neuron. 104: 501-511. DOI: 10.2210/Pdb6Pv8/Pdb  0.255
2018 Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, Del Cano L, Jiménez A, Martínez M, Melero R, Majtner T, Maluenda D, Mota J, Rancel Y, Ramírez-Aportela E, Vilas JL, Carroni M, Fleischmann S, ... Lindahl E, et al. Using Scipion for Stream Image Processing at Cryo-EM Facilities. Journal of Structural Biology. PMID 30296492 DOI: 10.1016/J.Jsb.2018.10.001  0.249
2015 Pronk S, Lindahl E, Kasson PM. Coupled diffusion in lipid bilayers upon close approach. Journal of the American Chemical Society. 137: 708-14. PMID 25535654 DOI: 10.1021/Ja508803D  0.248
2008 Lindahl ER. Molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 443: 3-23. PMID 18446279 DOI: 10.1007/978-1-59745-177-2_1  0.241
2017 Pouya I, Pronk S, Lundborg M, Lindahl E. Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling Future Generation Computer Systems. 71: 18-31. DOI: 10.1016/J.Future.2016.11.004  0.241
2018 Nakane T, Kimanius D, Lindahl E, Scheres SH. Author response: Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION Elife. DOI: 10.7554/Elife.36861.022  0.24
2007 Kutzner C, van der Spoel D, Fechner M, Lindahl E, Schmitt UW, de Groot BL, Grubmüller H. Speeding up parallel GROMACS on high-latency networks. Journal of Computational Chemistry. 28: 2075-84. PMID 17405124 DOI: 10.1002/Jcc.20703  0.237
2023 Yvonnesdotter L, Rovšnik U, Blau C, Lycksell M, Howard RJ, Lindahl E. Automated simulation-based membrane-protein refinement into cryo-EM data. Biophysical Journal. PMID 37277992 DOI: 10.1016/j.bpj.2023.05.033  0.234
2015 Lindahl E. Molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 1215: 3-26. PMID 25330956 DOI: 10.1007/978-1-4939-1465-4_1  0.234
2013 Nyblom M, Poulsen H, Gourdon P, Reinhard L, Andersson M, Lindahl E, Fedosova N, Nissen P. Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state. Science (New York, N.Y.). 342: 123-7. PMID 24051246 DOI: 10.1126/Science.1243352  0.232
2022 Mehregan A, Pérez-Conesa S, Zhuang Y, Elbahnsi A, Pasini D, Lindahl E, Howard RJ, Ulens C, Delemotte L. Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium. Biochimica Et Biophysica Acta. Biomembranes. 183994. PMID 35724739 DOI: 10.1016/j.bbamem.2022.183994  0.23
2023 Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E. Structure and dynamics of differential ligand binding in the human ρ-type GABA receptor. Neuron. PMID 37659407 DOI: 10.1016/j.neuron.2023.08.006  0.23
2018 Blau C, Lindahl E. Molecule Mechanics from Cryo-EM Images and Multiple Reconstructed Densities Biophysical Journal. 114: 50a. DOI: 10.1016/J.Bpj.2017.11.326  0.226
2016 Heusser SA, Howard RJ, Pouya I, Klement G, Borghese C, Harris RA, Lindahl E. A Single Mutation in GLIC Reveals Both the Potentiating and the Inhibitory Nature of Propofol Biophysical Journal. 110: 456a. DOI: 10.1016/J.Bpj.2015.11.2445  0.225
2017 Blau C, Lindahl E. All-Atom Ensemble Refinement to Cryo-EM Densities with a Bayesian Measure of Goodness-Of-Fit Biophysical Journal. 112: 575a. DOI: 10.1016/J.Bpj.2016.11.3095  0.219
2006 Kutzner C, Spoel Dvd, Fechner M, Lindahl E, Schmitt UW, Groot BLd, Grubmüller H. Improved GROMACS scaling on ethernet switched clusters Lecture Notes in Computer Science. 404-405. DOI: 10.1007/11846802_57  0.216
2021 Gossen J, Albani S, Hanke A, Joseph BP, Bergh C, Kuzikov M, Costanzi E, Manelfi C, Storici P, Gribbon P, Beccari AR, Talarico C, Spyrakis F, Lindahl E, Zaliani A, et al. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics. Acs Pharmacology & Translational Science. 4: 1079-1095. PMID 34136757 DOI: 10.1021/acsptsci.0c00215  0.21
2022 Bondarenko V, Wells MM, Chen Q, Tillman TS, Singewald K, Lawless MJ, Caporoso J, Brandon N, Coleman JA, Saxena S, Lindahl E, Xu Y, Tang P. Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor. Nature Communications. 13: 793. PMID 35145092 DOI: 10.1038/s41467-022-28400-x  0.206
2018 de la Rosa-Trevín JM, Gómez-Blanco J, Conesa P, Rancel Y, del Cano L, Arranz R, Chichón FJ, Martín-Benito J, Carroni M, Fleichman S, Lindahl E, Basham M, Clare DK, Savage K, Siebert CA, et al. Using Scipion for stream image processing at cryo-EM facilities Acta Crystallographica Section a Foundations and Advances. 74: a161-a161. DOI: 10.1107/S0108767318098380  0.206
2019 Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, et al. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell. PMID 30827889 DOI: 10.1016/J.Ccell.2019.01.020  0.205
2022 Zhu S, Sridhar A, Teng J, Howard RJ, Lindahl E, Hibbs RE. Structural and dynamic mechanisms of GABA receptor modulators with opposing activities. Nature Communications. 13: 4582. PMID 35933426 DOI: 10.1038/s41467-022-32212-4  0.195
2023 Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. Biorxiv : the Preprint Server For Biology. PMID 37205542 DOI: 10.1101/2023.05.02.538537  0.191
2019 Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, et al. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell. 36: 690-691. PMID 31821785 DOI: 10.1016/J.Ccell.2019.11.008  0.187
2022 Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews. Computational Molecular Science. e1622. PMID 35935573 DOI: 10.1002/wcms.1622  0.182
2023 Blau C, Yvonnesdotter L, Lindahl E. Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach. Plos Computational Biology. 19: e1011255. PMID 37523411 DOI: 10.1371/journal.pcbi.1011255  0.182
2020 Páll S, Zhmurov A, Bauer P, Abraham M, Lundborg M, Gray A, Hess B, Lindahl E. Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS. The Journal of Chemical Physics. 153: 134110. PMID 33032406 DOI: 10.1063/5.0018516  0.177
2018 Eriksson O, Laure E, Lindahl E, Henningson DS, Ynnerman A. e-Science in Scandinavia Informatik Spektrum. 41: 398-404. DOI: 10.1007/S00287-018-01133-2  0.177
2013 Bertaccini EJ, Yoluk O, Lindahl ER, Trudell JR. Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor. Anesthesiology. 119: 1087-95. PMID 23770602 DOI: 10.1097/ALN.0b013e31829e47e3  0.171
2024 Yu X, Matico RE, Miller R, Chauhan D, Van Schoubroeck B, Grauwen K, Suarez J, Pietrak B, Haloi N, Yin Y, Tresadern GJ, Perez-Benito L, Lindahl E, Bottelbergs A, Oehlrich D, et al. Structural basis for the oligomerization-facilitated NLRP3 activation. Nature Communications. 15: 1164. PMID 38326375 DOI: 10.1038/s41467-024-45396-8  0.163
2020 Masrati G, Mondal R, Rimon A, Kessel A, Padan E, Lindahl E, Ben-Tal N. An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transporters. Proceedings of the National Academy of Sciences of the United States of America. PMID 33257549 DOI: 10.1073/pnas.2002710117  0.163
2021 van Sorge NM, Bonsor DA, Deng L, Lindahl E, Schmitt V, Lyndin M, Schmidt A, Nilsson OR, Brizuela J, Boero E, Sundberg EJ, van Strijp JAG, Doran KS, Singer BB, Lindahl G, et al. Bacterial protein domains with a novel Ig-like fold target human CEACAM receptors. The Embo Journal. e106103. PMID 33522633 DOI: 10.15252/embj.2020106103  0.16
2023 Wennberg C, Lundborg M, Lindahl E, Norlén L. Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 37462219 DOI: 10.1021/acs.jcim.3c00625  0.154
2022 Oruganti B, Lindahl E, Yang J, Amiri W, Rahimullah R, Friedman R. Allosteric Enhancement of the BCR-Abl1 Kinase Inhibition Activity of Nilotinib by Co-Binding of Asciminib. The Journal of Biological Chemistry. 102238. PMID 35809644 DOI: 10.1016/j.jbc.2022.102238  0.154
2020 Narangifard A, Wennberg CL, Hollander LD, Iwai I, Han H, Lundborg M, Masich S, Lindahl E, Daneholt B, Norlén L. Molecular reorganization during formation of the human skin barrier studied in situ. The Journal of Investigative Dermatology. PMID 33098827 DOI: 10.1016/j.jid.2020.07.040  0.153
2023 Haloi N, Huang S, Nichols AN, Fine EJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA. Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. Biorxiv : the Preprint Server For Biology. PMID 36712031 DOI: 10.1101/2023.01.16.524298  0.152
2023 Legesse DH, Fan C, Teng J, Zhuang Y, Howard RJ, Noviello CM, Lindahl E, Hibbs RE. Structural insights into opposing actions of neurosteroids on GABA receptors. Nature Communications. 14: 5091. PMID 37607940 DOI: 10.1038/s41467-023-40800-1  0.151
2024 Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA. Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. Protein Engineering, Design & Selection : Peds. PMID 38302088 DOI: 10.1093/protein/gzae003  0.148
2022 Lundborg M, Wennberg C, Lidmar J, Hess B, Lindahl E, Norlén L. Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophysical Journal. PMID 36104960 DOI: 10.1016/j.bpj.2022.09.009  0.138
2020 de la Rosa-Trevín JM, Hernández Viga PA, Otón J, Lindahl E. Development of basic building blocks for cryo-EM: the emcore and emvis software libraries. Acta Crystallographica. Section D, Structural Biology. 76: 350-356. PMID 32254059 DOI: 10.1107/S2059798320003769  0.131
2019 Kimanius D, Lindahl ER, Andersson M. Uptake Dynamics in the Lactose Permease (LacY) Membrane Protein Transporter Biophysical Journal. 116: 555a. DOI: 10.1016/j.bpj.2018.11.2986  0.131
2022 Xu Y, Zhang S, Lindahl E, Friedman R, Wu W, Su P. A general tight-binding based energy decomposition analysis scheme for intermolecular interactions in large molecules. The Journal of Chemical Physics. 157: 034104. PMID 35868936 DOI: 10.1063/5.0091781  0.118
2020 Dávila-Rodríguez MJ, Freire TS, Lindahl E, Caracelli I, Zukerman-Schpector J, Friedman R. Is breaking of a hydrogen bond enough to lead to drug resistance? Chemical Communications (Cambridge, England). PMID 32424388 DOI: 10.1039/D0Cc02164D  0.093
2013 Åström JA, Carter A, Hetherington J, Ioakimidis K, Lindahl E, Mozdzynski G, Nash RW, Schlatter P, Signell A, Westerholm J. Preparing scientific application software for exascale computing Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7782: 27-42. DOI: 10.1007/978-3-642-36803-5_2  0.077
2019 Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, et al. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell. 35: 816. PMID 31085179 DOI: 10.1016/j.ccell.2019.04.011  0.03
2009 Lindahl E, Ottosson M, Carlsson J. Atomic Layer Deposition of NiO by the Ni(thd)2/H2O Precursor Combination Chemical Vapor Deposition. 15: 186-191. DOI: 10.1002/cvde.200906762  0.028
1935 Lindahl E. Arbetslöshet och finanspolitik Ekonomisk Tidskrift. 37: 1. DOI: 10.2307/3438036  0.018
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