Erik Lindahl - Publications

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131 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  1
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  1
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  1
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  1
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  1
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  0.01
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  1
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  0.01
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  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.04
2019 Bowman GR, Lindahl E. Decision letter: The dynamic conformational landscape of the protein methyltransferase SETD8 Elife. DOI: 10.7554/Elife.45403.074  0.01
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  1
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  1
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  1
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  1
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  1
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  0.01
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  0.01
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  1
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  0.01
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  1
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  1
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  0.01
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  0.01
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  1
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  1
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  1
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  0.01
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  1
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  0.01
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  0.01
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  1
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  1
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  1
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  0.12
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  1
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  0.01
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  1
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  1
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  1
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  1
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  1
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  0.01
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  1
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  0.01
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  1
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  1
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  0.01
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  0.01
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  1
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  0.01
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  1
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  0.01
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  1
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  1
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  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.01
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  1
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  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.01
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  1
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  1
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  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  1
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  0.01
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  1
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  0.01
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  1
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  0.01
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  1
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  0.01
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  0.01
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  1
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  1
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  0.01
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  1
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  1
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  0.01
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  0.01
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  0.01
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  0.01
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  1
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  0.01
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  0.01
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  0.01
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  1
1998 Lindahl E, Edholm O. Solvent diffusion outside macromolecular surfaces Physical Review E. 57: 791-796. DOI: 10.1103/Physreve.57.791  0.01
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