List of works - Erik Lindahl

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

scientific article published on 19 February 2009

3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures

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

scientific article

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

article

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

scientific article published on 25 October 2017

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

scientific article

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

scientific article

Algorithm improvements for molecular dynamics simulations

article

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

scientific article published on 29 September 2006

An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations

scientific article

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

scientific article

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.

scientific article

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

scientific article

Copernicus

Correction to the article “Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations”

scholarly article by Anna C. V. Johansson published in January 2008

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

scientific article published on 22 September 2017

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

scientific article published on 31 March 2020

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

scientific article

Functional characterization of neurotransmitter activation and modulation in a nematode model ligand-gated ion channel.

scientific article published on 22 April 2016

GROMACS 3.0: a package for molecular simulation and trajectory analysis

article

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

scientific article

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

scientific article (publication date: March 2008)

GROMACS: fast, flexible, and free

scientific article (publication date: December 2005)

Gas-Pulsed CVD for Film Growth in the CuNiN System

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

scientific article published on 01 October 2020

Identification of related proteins on family, superfamily and fold level

scientific article published in January 2000

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

scientific article

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

scientific article published on 25 January 2010

Improved model quality assessment using ProQ2.

scientific article

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

scientific article published on 25 July 2013

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

scientific article

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale

scientific article published on 01 July 2024

Membrane proteins diffuse as dynamic complexes with lipids.

scientific article

Membrane proteins: molecular dynamics simulations.

scientific article published on 10 April 2008

Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor

scientific article

Model quality assessment for membrane proteins ⬇️

scientific article published on October 14, 2010

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

scientific article

Molecular basis for voltage sensitivity in membrane proteins

Molecular dynamics simulation of NMR relaxation rates and slow dynamics in lipid bilayers

article

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

scientific article

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

scientific article published on 9 January 2012

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

scientific article published on July 2006

New tools for automated high-resolution cryo-EM structure determination in RELION-3

scientific article published on 09 November 2018

Normal mode analysis reveals the channel gating motion within a ligand gated ion channel model

article

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

scientific article published on 11 June 2010

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

scientific article published on July 2006

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

scientific article

Prediction of membrane-protein topology from first principles

scholarly article

Preparing Scientific Application Software for Exascale Computing

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

scientific article

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

scientific article published on September 2009

RELION-3: new tools for automated high-resolution cryo-EM structure determination

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

scientific article

Simulation of the Spontaneous Aggregation of Phospholipids into Bilayers

scientific article published on 01 September 2001

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

scientific article

Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations

article

Speeding up parallel GROMACS on high-latency networks

scientific article

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

scientific article

Structure of the human ClC-1 chloride channel

scientific article published on 25 April 2019

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

scientific article published in January 2019

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

scientific article published on 8 January 2013

The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain

scientific article

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

scientific article

Titratable Amino Acid Solvation in Lipid Membranes as a Function of Protonation State

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

scientific article

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

scientific article published on 04 August 2023

Unraveling the strokes of ion channel molecular machines in computers

scientific article published on 10 December 2012

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

scientific article published on 25 April 2008

Water ordering at membrane interfaces controls fusion dynamics

scientific article

List of works by Erik Lindahl

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

3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures

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

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

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

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

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

Algorithm improvements for molecular dynamics simulations

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

An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations

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

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.

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

Copernicus

Correction to the article “Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations”

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

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

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

Functional characterization of neurotransmitter activation and modulation in a nematode model ligand-gated ion channel.

GROMACS 3.0: a package for molecular simulation and trajectory analysis

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

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

GROMACS: fast, flexible, and free

Gas-Pulsed CVD for Film Growth in the CuNiN System

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

Identification of related proteins on family, superfamily and fold level

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

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

Improved model quality assessment using ProQ2.

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

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

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale

Membrane proteins diffuse as dynamic complexes with lipids.

Membrane proteins: molecular dynamics simulations.

Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor

Model quality assessment for membrane proteins ⬇️

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

Molecular basis for voltage sensitivity in membrane proteins

Molecular dynamics simulation of NMR relaxation rates and slow dynamics in lipid bilayers

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

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

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

New tools for automated high-resolution cryo-EM structure determination in RELION-3

Normal mode analysis reveals the channel gating motion within a ligand gated ion channel model

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

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

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

Prediction of membrane-protein topology from first principles

Preparing Scientific Application Software for Exascale Computing

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

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

RELION-3: new tools for automated high-resolution cryo-EM structure determination

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

Simulation of the Spontaneous Aggregation of Phospholipids into Bilayers

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

Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations

Speeding up parallel GROMACS on high-latency networks

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

Structure of the human ClC-1 chloride channel

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

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

The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain

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

Titratable Amino Acid Solvation in Lipid Membranes as a Function of Protonation State

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

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

Unraveling the strokes of ion channel molecular machines in computers

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

Water ordering at membrane interfaces controls fusion dynamics