Erik Lindahl

Erik Lindahl

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Erik Lindahl

Publications by authors named "Erik Lindahl"

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Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor.

Neuron 2019 Nov 2;104(3):501-511.e6. Epub 2019 Sep 2.

Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2019.07.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842111PMC
November 2019

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces.

Bioinformatics 2019 Sep;35(18):3505-3507

Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btz104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748756PMC
September 2019

Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope.

Proc Natl Acad Sci U S A 2019 May 26;116(20):10009-10018. Epub 2019 Apr 26.

Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain;

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http://dx.doi.org/10.1073/pnas.1821442116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525488PMC
May 2019

Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair.

Cancer Cell 2019 03 28;35(3):504-518.e7. Epub 2019 Feb 28.

Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2019.01.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424615PMC
March 2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.

PLoS Comput Biol 2019 01 17;15(1):e1006649. Epub 2019 Jan 17.

Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006649DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336246PMC
January 2019

Determining the molecular basis of voltage sensitivity in membrane proteins.

J Gen Physiol 2018 10 27;150(10):1444-1458. Epub 2018 Aug 27.

Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden

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http://dx.doi.org/10.1085/jgp.201812086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168238PMC
October 2018

Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity.

Proc Natl Acad Sci U S A 2018 10 1;115(42):10672-10677. Epub 2018 Oct 1.

Department of Biochemistry and Biophysics, Stockholm University, 11419 Stockholm, Sweden;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1809650115
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http://dx.doi.org/10.1073/pnas.1809650115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196478PMC
October 2018

Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation.

J Struct Biol 2018 08 24;203(2):149-161. Epub 2018 Apr 24.

Department of Cell and Molecular Biology (CMB), Karolinska Institute, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2018.04.005DOI Listing
August 2018

Predicting drug permeability through skin using molecular dynamics simulation.

J Control Release 2018 08 1;283:269-279. Epub 2018 Jun 1.

Department of Cell and Molecular Biology (CMB), Karolinska Institute, Solna, Sweden; Dermatology Clinic, Karolinska University Hospital, Solna, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.jconrel.2018.05.026DOI Listing
August 2018

Publisher Correction: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Nat Plants 2018 08;4(8):615

Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1038/s41477-018-0203-0DOI Listing
August 2018

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Nat Plants 2018 04 2;4(4):212-217. Epub 2018 Apr 2.

Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1038/s41477-018-0129-6DOI Listing
April 2018

Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels.

Cell Rep 2018 04;23(4):993-1004

Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.108DOI Listing
April 2018

Structural Transitions in Ceramide Cubic Phases during Formation of the Human Skin Barrier.

Biophys J 2018 03;114(5):1116-1127

Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biophysics and Biochemistry, Science for Life Laboratory, Stockholm University, Solna, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.12.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883571PMC
March 2018

Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h.

IUCrJ 2017 Nov 22;4(Pt 6):723-727. Epub 2017 Sep 22.

Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden.

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http://dx.doi.org/10.1107/S205225251701226XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668856PMC
November 2017

A drug pocket at the lipid bilayer-potassium channel interface.

Sci Adv 2017 10 25;3(10):e1701099. Epub 2017 Oct 25.

Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1126/sciadv.1701099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656419PMC
October 2017

Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport.

Biophys J 2016 Dec;111(11):2417-2429

Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.10.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5153542PMC
December 2016

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.

Elife 2016 11 15;5. Epub 2016 Nov 15.

Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.7554/eLife.18722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5310839PMC
November 2016

Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids.

Proc Natl Acad Sci U S A 2016 09 6;113(38):10559-64. Epub 2016 Sep 6.

Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden; Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden

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http://www.pnas.org/content/early/2016/09/01/1606776113.full
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http://www.pnas.org/lookup/doi/10.1073/pnas.1606776113
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035864PMC
http://dx.doi.org/10.1073/pnas.1606776113DOI Listing
September 2016

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.

Nat Commun 2016 08 31;7:12575. Epub 2016 Aug 31.

Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.

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http://dx.doi.org/10.1038/ncomms12575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013691PMC
August 2016

Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation.

Sci Rep 2016 06 9;6:27562. Epub 2016 Jun 9.

Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1038/srep27562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899724PMC
June 2016

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel.

PLoS Comput Biol 2016 Jan 11;12(1):e1004704. Epub 2016 Jan 11.

Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1004704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709198PMC
January 2016

Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation.

J Chem Theory Comput 2015 Dec 20;11(12):5737-46. Epub 2015 Nov 20.

Swedish e-Science Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 171 21 Solna, Sweden.

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http://dx.doi.org/10.1021/acs.jctc.5b00726DOI Listing
December 2015

Dynamic heterogeneity controls diffusion and viscosity near biological interfaces.

Nat Commun 2014 ;5:3034

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1038/ncomms4034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971065PMC
November 2015

Conformational gating dynamics in the GluCl anion-selective chloride channel.

ACS Chem Neurosci 2015 Aug 2;6(8):1459-67. Epub 2015 Jun 2.

†Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden.

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http://dx.doi.org/10.1021/acschemneuro.5b00111DOI Listing
August 2015

SAXS-Guided Metadynamics.

J Chem Theory Comput 2015 Jul;11(7):3491-8

Department of Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology , SE-171 21 Solna, Sweden.

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http://dx.doi.org/10.1021/acs.jctc.5b00299DOI Listing
July 2015

Molecular dynamics simulations.

Authors:
Erik Lindahl

Methods Mol Biol 2015 ;1215:3-26

Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91, Stockholm, Sweden,

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http://dx.doi.org/10.1007/978-1-4939-1465-4_1DOI Listing
June 2015

Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

J Chem Theory Comput 2015 Jun;11(6):2600-8

Swedish eScience Research Center, Department of Theoretical Physics, KTH Royal Institute of Technology , SE-100 44 Stockholm, Sweden.

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http://dx.doi.org/10.1021/acs.jctc.5b00234DOI Listing
June 2015

Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.

J Phys Chem B 2015 Jan 7;119(3):810-23. Epub 2014 Nov 7.

Department of Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, Royal Institute of Technology , SE-171 21 Solna, Sweden.

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http://pubs.acs.org/doi/10.1021/jp505332p
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http://dx.doi.org/10.1021/jp505332pDOI Listing
January 2015

Coupled diffusion in lipid bilayers upon close approach.

J Am Chem Soc 2015 Jan 6;137(2):708-14. Epub 2015 Jan 6.

'Department of Theoretical Physics, KTH Royal Institute of Technology , AlbaNova, 106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1021/ja508803dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308745PMC
January 2015

Structural models of ligand-gated ion channels: sites of action for anesthetics and ethanol.

Alcohol Clin Exp Res 2014 Mar 24;38(3):595-603. Epub 2013 Oct 24.

Department of Molecular & Medical Pharmacology , David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Anesthesiology , David Geffen School of Medicine at UCLA, Los Angeles, California.

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http://dx.doi.org/10.1111/acer.12283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959612PMC
March 2014

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations.

J Comput Chem 2014 Jan 20;35(3):260-9. Epub 2013 Nov 20.

Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Science for Life Laboratory, Box 1031, SE-171 21, Solna, Sweden.

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http://dx.doi.org/10.1002/jcc.23495DOI Listing
January 2014

Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor.

Anesthesiology 2013 Nov;119(5):1087-95

* Professor, Department of Anesthesia, Stanford University School of Medicine, Stanford, California, and Anesthesiologist and Intensivist, Palo Alto VA Health Care System, Palo Alto, California. † Doctoral Candidate, ‡ Professor of Computational Structural Biology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. § Professor of Chemistry in Anesthesia, Department of Anesthesia, Stanford University School of Medicine.

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http://dx.doi.org/10.1097/ALN.0b013e31829e47e3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823821PMC
November 2013

Functional validation of virtual screening for novel agents with general anesthetic action at ligand-gated ion channels.

Mol Pharmacol 2013 Nov 15;84(5):670-8. Epub 2013 Aug 15.

Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland (S.A.H.); Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas (R.J.H., C.M.B., M.A.C., U.S.L., R.A.H.); Science for Life Laboratory, KTH Royal Institute of Technology and Stockholm University, Stockholm, Sweden (T.B., E.L.); and Department of Biochemistry and Biophysics, Center for Biomembrane Research, Science for Life Laboratory, Stockholm University, Stockholm, Sweden (J.C.).

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http://dx.doi.org/10.1124/mol.113.087692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807073PMC
November 2013

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.

Arch Biochem Biophys 2013 Nov 12;539(1):20-30. Epub 2013 Sep 12.

Laboratório Nacional de Biociências (LNBio), Centro de Pesquisas em Energia e Materiais (CNPEM), Campinas, SP, Brazil.

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http://dx.doi.org/10.1016/j.abb.2013.09.003DOI Listing
November 2013

Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state.

Science 2013 Oct 19;342(6154):123-7. Epub 2013 Sep 19.

Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, DK-8000 Aarhus, Denmark.

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http://dx.doi.org/10.1126/science.1243352DOI Listing
October 2013

Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane.

J Am Chem Soc 2013 Sep 29;135(36):13590-7. Epub 2013 Aug 29.

Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology , SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1021/ja407326nDOI Listing
September 2013

Inhibition versus potentiation of ligand-gated ion channels can be altered by a single mutation that moves ligands between intra- and intersubunit sites.

Structure 2013 Aug 25;21(8):1307-16. Epub 2013 Jul 25.

Science for Life Laboratory, KTH Royal Institute of Technology & Stockholm University, 17121 Solna, Sweden.

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http://dx.doi.org/10.1016/j.str.2013.06.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787718PMC
August 2013

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties.

J Chem Theory Comput 2013 Aug 9;9(8):3527-37. Epub 2013 Jul 9.

Swedish e-Science Research Center and Department of Theoretical Physics, KTH Royal Institute of Technology , Box 1031, 17121 Solna, Sweden.

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http://pubs.acs.org/doi/10.1021/ct400140n
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http://dx.doi.org/10.1021/ct400140nDOI Listing
August 2013

Stabilization of the GluCl ligand-gated ion channel in the presence and absence of ivermectin.

Biophys J 2013 Aug;105(3):640-7

Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.

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http://dx.doi.org/10.1016/j.bpj.2013.06.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736686PMC
August 2013

Molecular mechanism for the dual alcohol modulation of Cys-loop receptors.

PLoS Comput Biol 2012 4;8(10):e1002710. Epub 2012 Oct 4.

Science for Life Laboratory, KTH Royal Institute of Technology & Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1002710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464191PMC
May 2013

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions.

Chem Phys Lipids 2013 Apr 12;169:106-12. Epub 2013 Jan 12.

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 29908, USA.

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http://dx.doi.org/10.1016/j.chemphyslip.2013.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631454PMC
April 2013

The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology.

Mol Membr Biol 2013 Mar 22;30(2):195-205. Epub 2012 Aug 22.

Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Denmark.

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http://dx.doi.org/10.3109/09687688.2012.713520DOI Listing
March 2013

The conserved phenylalanine in the K+ channel voltage-sensor domain creates a barrier with unidirectional effects.

Biophys J 2013 Jan 8;104(1):75-84. Epub 2013 Jan 8.

Science for Life Laboratory and Swedish e-Science Research Center, KTH Royal Institute of Technology and Stockholm University, Solna, Sweden.

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http://dx.doi.org/10.1016/j.bpj.2012.11.3827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540256PMC
January 2013

Unraveling the strokes of ion channel molecular machines in computers.

Authors:
Erik Lindahl

Proc Natl Acad Sci U S A 2012 Dec 10;109(52):21186-7. Epub 2012 Dec 10.

Science for Life Laboratory, 17121 SE-171 21 Solna, Sweden.

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http://dx.doi.org/10.1073/pnas.1218763110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535601PMC
December 2012

Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp.

ChemMedChem 2012 Oct 30;7(10):1775-83. Epub 2012 Mar 30.

Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, Am Fassberg 11, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1002/cmdc.201100600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525944PMC
October 2012

Improved model quality assessment using ProQ2.

BMC Bioinformatics 2012 Sep 10;13:224. Epub 2012 Sep 10.

Department of Theoretical Physics & Swedish eScience Research Center, Royal Institute of Technology, Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-13-224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584948PMC
September 2012

Tracking a complete voltage-sensor cycle with metal-ion bridges.

Proc Natl Acad Sci U S A 2012 May 25;109(22):8552-7. Epub 2012 Apr 25.

Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, SE-581 85 Linköping, Sweden.

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http://dx.doi.org/10.1073/pnas.1116938109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365220PMC
May 2012

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain.

Nature 2012 Jan 9;481(7382):525-9. Epub 2012 Jan 9.

Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature10742DOI Listing
January 2012

Structural basis for alcohol modulation of a pentameric ligand-gated ion channel.

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):12149-54. Epub 2011 Jul 5.

Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1104480108
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http://dx.doi.org/10.1073/pnas.1104480108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141919PMC
July 2011

Water ordering at membrane interfaces controls fusion dynamics.

J Am Chem Soc 2011 Mar 25;133(11):3812-5. Epub 2011 Feb 25.

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States.

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http://dx.doi.org/10.1021/ja200310dDOI Listing
March 2011

3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state.

Biophys J 2011 Mar;100(6):1446-54

Theoretical and Computational Biophysics, Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.bpj.2011.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059565PMC
March 2011

Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare.

Protein Sci 2010 Dec;19(12):2305-18

CBR,DBB,SBC, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1002/pro.510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009398PMC
December 2010

Model quality assessment for membrane proteins.

Bioinformatics 2010 Dec 14;26(24):3067-74. Epub 2010 Oct 14.

Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btq581DOI Listing
December 2010

Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM4.

J Chem Inf Model 2010 Dec 30;50(12):2248-55. Epub 2010 Nov 30.

Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California, United States.

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http://dx.doi.org/10.1021/ci100266cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010460PMC
December 2010

A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescaling.

J Comput Chem 2010 Nov;31(14):2593-600

Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://doi.wiley.com/10.1002/jcc.21552
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http://dx.doi.org/10.1002/jcc.21552DOI Listing
November 2010

Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model.

ACS Chem Neurosci 2010 Aug 11;1(8):552-8. Epub 2010 Jun 11.

Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1021/cn100026tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399477PMC
August 2010

Membrane proteins diffuse as dynamic complexes with lipids.

J Am Chem Soc 2010 Jun;132(22):7574-5

VTT Technical Research Center of Finland, Espoo, Finland.

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http://dx.doi.org/10.1021/ja101481bDOI Listing
June 2010

Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.

PLoS Comput Biol 2010 Jun 24;6(6):e1000829. Epub 2010 Jun 24.

Department of Chemistry, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891707PMC
June 2010

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

J Chem Theory Comput 2010 Feb 25;6(2):459-66. Epub 2010 Jan 25.

Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, and Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/ct900549rDOI Listing
February 2010

Protein contents in biological membranes can explain abnormal solvation of charged and polar residues.

Proc Natl Acad Sci U S A 2009 Sep 1;106(37):15684-9. Epub 2009 Sep 1.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0905394106
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747180PMC
September 2009

The role of lipid composition for insertion and stabilization of amino acids in membranes.

J Chem Phys 2009 May;130(18):185101

Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1063/1.3129863DOI Listing
May 2009

Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel.

PLoS Comput Biol 2009 Feb 20;5(2):e1000289. Epub 2009 Feb 20.

Center for Biomembrane Research & Stockholm Bioinformatics Center, Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1000289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632863PMC
February 2009

3D pressure field in lipid membranes and membrane-protein complexes.

Phys Rev Lett 2009 Feb 19;102(7):078101. Epub 2009 Feb 19.

Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland.

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http://dx.doi.org/10.1103/PhysRevLett.102.078101DOI Listing
February 2009

Titratable amino acid solvation in lipid membranes as a function of protonation state.

J Phys Chem B 2009 Jan;113(1):245-53

Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1021/jp8048873DOI Listing
January 2009

Membrane proteins: molecular dynamics simulations.

Curr Opin Struct Biol 2008 Aug 10;18(4):425-31. Epub 2008 Apr 10.

Department of Biochemistry & Biophysics, SCenter for Biomembrane Research & Stockholm Bioinformatics Center, tockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.sbi.2008.02.003DOI Listing
August 2008

Using multiple templates to improve quality of homology models in automated homology modeling.

Protein Sci 2008 Jun 25;17(6):990-1002. Epub 2008 Apr 25.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1110/ps.073344908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386743PMC
June 2008

Molecular dynamics simulations.

Authors:
Erik R Lindahl

Methods Mol Biol 2008 ;443:3-23

Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

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http://dx.doi.org/10.1007/978-1-59745-177-2_1DOI Listing
June 2008

Prediction of membrane-protein topology from first principles.

Proc Natl Acad Sci U S A 2008 May 13;105(20):7177-81. Epub 2008 May 13.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0711151105
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438223PMC
May 2008

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein.

J Chem Inf Model 2008 Apr 19;48(4):855-60. Epub 2008 Mar 19.

Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305-5117, USA.

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http://dx.doi.org/10.1021/ci700456sDOI Listing
April 2008

Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.

Proteins 2008 Mar;70(4):1332-44

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1002/prot.21629DOI Listing
March 2008

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

J Chem Theory Comput 2008 Mar;4(3):435-47

Max-Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany.

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http://pubs.acs.org/doi/abs/10.1021/ct700301q
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March 2008

Normal-mode analysis of the glycine alpha1 receptor by three separate methods.

J Chem Inf Model 2007 Jul-Aug;47(4):1572-9. Epub 2007 Jun 30.

Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305-5117, USA.

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http://dx.doi.org/10.1021/ci600566jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2530920PMC
October 2007

Speeding up parallel GROMACS on high-latency networks.

J Comput Chem 2007 Sep;28(12):2075-84

Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1002/jcc.20703DOI Listing
September 2007

Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations.

Biophys J 2006 Dec 29;91(12):4450-63. Epub 2006 Sep 29.

Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S000634950672157
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http://dx.doi.org/10.1529/biophysj.106.092767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779925PMC
December 2006

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W38-42

Unité de Dynamique Structurale des Macromolécules, URA 2185 du C.N.R.S., Institut Pasteur, 75015 Paris, France.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538897PMC
July 2006

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W52-6

Unite de Dynamique Structurale des Macromolécules, URA 2185 du C.N.R.S., Institut Pasteur, 75015 Paris, France.

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http://dx.doi.org/10.1093/nar/gkl082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538881PMC
July 2006

GROMACS: fast, flexible, and free.

J Comput Chem 2005 Dec;26(16):1701-18

Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden.

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http://dx.doi.org/10.1002/jcc.20291DOI Listing
December 2005

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization.

Nucleic Acids Res 2005 8;33(14):4496-506. Epub 2005 Aug 8.

Unité de Biochimie Structurale, URA 2185 du CNRS, Institut Pasteur 25 Rue du Dr Roux, F-75015 Paris, France.

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http://dx.doi.org/10.1093/nar/gki730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183489PMC
August 2005

Simulations of the role of water in the protein-folding mechanism.

Proc Natl Acad Sci U S A 2004 Apr 16;101(17):6456-61. Epub 2004 Apr 16.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.0307898101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC404066PMC
April 2004

Molecular dynamics simulations of phospholipid bilayers with cholesterol.

Biophys J 2003 Apr;84(4):2192-206

Theoretical Biophysics, Royal Institute of Technology, Stockholm Center for Physics, Astronomy and Biotechnology, SE-106 91 Stockholm, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302786PMC
http://dx.doi.org/10.1016/S0006-3495(03)75025-5DOI Listing
April 2003