List of works by Mark S.P. Sansom

A BEST example of channel structure annotation by molecular simulation.

scientific article published on 20 March 2017

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry

scientific article published on 14 December 2015

A Kv channel with an altered activation gate sequence displays both "fast" and "slow" activation kinetics.

scientific article

A conformational landscape for alginate secretion across the outer membrane ofPseudomonas aeruginosa

scientific article

A conserved tryptophan at the membrane-water interface acts as a gatekeeper for Kir6.2/SUR1 channels and causes neonatal diabetes when mutated.

scientific article published on 3 May 2011

A generalized born implicit-membrane representation compared to experimental insertion free energies.

scientific article published on 11 January 2007

A helix heterodimer in a lipid bilayer: prediction of the structure of an integrin transmembrane domain via multiscale simulations.

scientific article published on October 2011

A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates

scientific article published on 24 June 2019

A hydrophobic barrier deep within the inner pore of the TWIK-1 K2P potassium channel

scientific article

A lipid gating mechanism for the channel-forming O antigen ABC transporter

scientific article published on 18 February 2019

A multiscale approach to modelling drug metabolism by membrane-bound cytochrome P450 enzymes

scientific article (publication date: July 2014)

A multiscale simulation study of carbon nanotube interactions with designed amphiphilic peptide helices

scientific article published on 09 April 2010

A novel congenital myasthenic syndrome due to decreased acetylcholine receptor ion-channel conductance.

scientific article

A prokaryotic glutamate receptor: homology modelling and molecular dynamics simulations of GluR0.

scientific article published in October 2003

A universally conserved residue in the SUR1 subunit of the KATP channel is essential for translating nucleotide binding at SUR1 into channel opening.

scientific article

Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter.

scientific article published on 28 January 2016

Acquisition of siderophores in gram-negative bacteria.

scientific article

Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class.

scientific article

Alamethicin and related peptaibols ? model ion channels ⬇️

scientific article published on 01 January 1993

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.

scientific article published on 14 May 2015

Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation

scientific article published on 01 July 2021

Amantadine blocks channel activity of the transmembrane segment of the NB protein from influenza B.

scientific article

An anion-selective analogue of the channel-forming peptide alamethicin

scientific article published on 01 May 1999

An atomic detail model for the human ATP binding cassette transporter P‐glycoprotein derived from disulphide cross‐ linking and homology modeling ⬇️

scientific article published on October 16, 2003

Analysis of post-perturbation gating kinetics of single ion channels.

scientific article published in February 1989

Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network

scientific article published in Scientific Reports

Anomalous Dynamics of a Lipid Recognition Protein on a Membrane Surface

scientific article

Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers ⬇️

scientific article published on 15 March 2016

Asymmetric Stability among the Transmembrane Helices of Lactose Permease†

article

Asymmetric mechanosensitivity in a eukaryotic ion channel.

scientific article published on 18 September 2017

Atomistic mechanism of transmembrane helix association

scientific article published on 04 June 2020

Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association

scientific article published on 9 February 2018

Band 3, the human red cell chloride/bicarbonate anion exchanger (AE1, SLC4A1), in a structural context. ⬇️

scientific article published on 5 April 2016

Bendix: intuitive helix geometry analysis and abstraction.

scientific article published on 23 June 2012

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.

scholarly article

Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel.

scientific article published on 24 March 2017

Binding of Ca 2+ -Independent C2 Domains to Lipid Membranes: a Multi-Scale Molecular Dynamics Study

Binding of Ca<sup>2+</sup>-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study

scientific article published on 02 June 2021

Binding site flexibility: molecular simulation of partial and full agonists within a glutamate receptor.

scientific article

Biomimetic Design of a Brush-Like Nanopore: Simulation Studies

scientific article published on 19 December 2011

Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study

scientific article published on 6 February 2017

Biomimetic water channels: general discussion

scientific article published on 01 September 2018

Biophysical and computational studies of membrane penetration by the GRP1 pleckstrin homology domain.

scientific article

Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study

scientific article published on 30 July 2008

Bundles Consisting of Extended Transmembrane Segments of Vpu from HIV-1: Computer Simulations and Conductance Measurements†

article

Carbon nanotube/detergent interactions via coarse-grained molecular dynamics

scientific article published on 09 June 2007

Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of Complexes III and IV

Channel gating: twist to open.

scientific article

Channels formed by the transmembrane helix of phospholamban: a simulation study

scientific article published on 01 December 1997

Chemical reactions in 2D: self-assembly and self-esterification of 9(10),16-dihydroxypalmitic acid on mica surface.

scientific article published in June 2009

Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System.

scientific article published on September 2009

Coarse-Grained Simulations Suggest the Epsin N-Terminal Homology Domain Can Sense Membrane Curvature without Its Terminal Amphipathic Helix

scientific article published on 10 December 2020

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

scientific article published in July 2009

Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces.

scientific article

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

scientific article

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

scientific article published on 20 October 2006

Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.

scientific article

Comparative molecular dynamics--similar folds and similar motions?

scientific article published on December 2005

Computational Modeling of Realistic Cell Membranes

scientific article published on 09 January 2019

Computational virology: From the inside out

scientific article

Conformation and environment of channel-forming peptides: a simulation study

scientific article

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

scientific article

Conformational Dynamics of a Lipid-Interacting Protein: MD Simulations of Saposin B†

article

Conformational change in an MFS protein: MD simulations of LacY

scientific article published on 01 July 2007

Conformational changes in talin on binding to anionic phospholipid membranes facilitate signaling by integrin transmembrane helices

scientific article

Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations.

scientific article published in November 2005

Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies.

scientific article

Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating.

scientific article published on 4 March 2005

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study.

scientific article

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

scientific article

Control of KirBac3.1 Potassium Channel Gating at the Interface between Cytoplasmic Domains

scientific article

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.

scientific article

Cryo-EM structure of the mechanically activated ion channel OSCA1.2

scientific article

Crystal Structures of the Extracellular Domain from PepT1 and PepT2 Provide Novel Insights into Mammalian Peptide Transport

scientific article

Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2

scientific article

Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels

scientific article published on 25 March 2020

Defining the membrane-associated state of the PTEN tumor suppressor protein.

scientific article

Designing biomimetic pores based on carbon nanotubes

scientific article

Detailed Examination of a Single Conduction Event in a Potassium Channel.

scientific article published on 29 August 2013

Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity. ⬇️

scientific article published on 20 January 2017

Dynamic role of the tether helix in PIP2-dependent gating of a G protein-gated potassium channel

scientific article published on 18 July 2017

Dynamics and function in a bacterial ABC transporter: simulation studies of the BtuCDF system and its components

scientific article published on 16 February 2007

Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes

scientific article published on 19 March 2021

Effect of the Southeast Asian Ovalocytosis Deletion on the Conformational Dynamics of Signal-Anchor Transmembrane Segment 1 of Red Cell Anion Exchanger 1 (AE1, Band 3, or SLC4A1).

scientific article published on 9 January 2017

Effective diffusion coefficients of K+ and Cl- ions in ion channel models

scientific article published on 01 June 1999

Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT 3 Receptor Channel

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

scientific article published on 19 July 2018

Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl − Channel

Electrostatics studies and molecular dynamics simulations of a homology model of the Shaker K+ channel pore.

scientific article published in August 2001

Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels.

scientific article published on 08 October 2013

Engineering stabilized ion channels: covalent dimers of alamethicin

scientific article published on 01 May 1996

Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques.

scientific article

Exploring peptide-membrane interactions with coarse-grained MD simulations.

scientific article published on April 2011

Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.

scientific article published in April 2003

Ferrocenoyl Derivatives of Alamethicin: Redox-Sensitive Ion Channels†

scientific article published on 01 February 1997

Finding a needle in a haystack: the role of electrostatics in target lipid recognition by PH domains.

scientific article published on 26 July 2012

Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA.

scientific article published on 28 April 2006

Flexible gates generate occluded intermediates in the transport cycle of LacY.

scientific article published on February 2014

Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations

scientific article

Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor

scientific article published on 24 April 2016

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

scientific article published on 16 March 2011

Functional Annotation of Ion Channel Structures by Molecular Simulation.

scientific article

Functional analysis of a structural model of the ATP-binding site of the KATP channel Kir6.2 subunit.

scientific article published on 13 January 2005

Functional characterization of a mutated chicken alpha7 nicotinic acetylcholine receptor subunit with a leucine residue inserted in transmembrane domain 2.

scientific article

Functional complementation and genetic deletion studies of KirBac channels: activatory mutations highlight gating-sensitive domains

scientific article

Gating at both ends and breathing in the middle: conformational dynamics of TolC.

scientific article

Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations.

scientific article published on 30 October 2015

Grid computing and biomolecular simulation.

scientific article published in August 2005

HOLE: a program for the analysis of the pore dimensions of ion channel structural models

scientific article (publication date: December 1996)

Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.

scientific article published on 11 September 2008

Heteromeric GABAAreceptor structures in positively-modulated active states

Homology modelling and molecular dynamics simulations: comparative studies of human aquaporin-1.

scientific article

How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain.

scientific article published on February 2007

How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins

scientific article published in Nature Communications

Hydrophilic surface maps of channel-forming peptides: analysis of amphipathic helices

scientific article published on 01 January 1993

Hydrophobic gating in ion channels

scientific article

Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins

Identification of a functionally important negatively charged residue within the second catalytic site of the SUR1 nucleotide-binding domains.

scientific article published in December 2004

Identification of the PIP2-binding site on Kir6.2 by molecular modelling and functional analysis.

scientific article published on 2 August 2007

Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system.

scientific article

In silico mutation of cysteine residues in the ligand-binding domain of an N-methyl-D-aspartate receptor

scientific article published on 01 February 2007

Influence of Electronic Polarization on the Binding of Anions to a Chloride-Pumping Rhodopsin

Influence of effective polarization on ion and water interactions within a biomimetic nanopore

Insertion and assembly of membrane proteins via simulation.

scientific article

Insight into the mechanism of inactivation and pH sensitivity in potassium channels from molecular dynamics simulations.

scientific article published on 18 June 2008

Insights into How Nucleotide-Binding Domains Power ABC Transport

scientific article

Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations

scientific article published on 17 September 2019

Interactions between a voltage sensor and a toxin via multiscale simulations.

scientific article

Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics. ⬇️

scientific article published on 13 July 2016

Interactions of a Bacterial Cu(I)-ATPase with a Complex Lipid Environment

scientific article published on 27 June 2018

Interactions of phosphatase and tensin homologue (PTEN) proteins with phosphatidylinositol phosphates: insights from molecular dynamics simulations of PTEN and voltage sensitive phosphatase.

scientific article published on 10 March 2014

Interactions of the pleckstrin homology domain with phosphatidylinositol phosphate and membranes: characterization via molecular dynamics simulations.

scientific article

Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.

scientific article published in August 2003

Interfacial activation of M37 lipase: A multi-scale simulation study.

scientific article published on 16 December 2016

Ion channel formation by synthetic analogues of staphylococcal δ-toxin

scientific article published on 01 June 1995

Ion channel formation by zervamicin-IIB. A molecular modelling study

scientific article published on 01 January 1993

Ion channel gates: comparative analysis of energy barriers.

scientific article

Ion channel gating: insights via molecular simulations.

scientific article published on November 2003

Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues.

scientific article published on December 1997

Ion channels formed by amphipathic helical peptides

scientific article published on 01 January 1991

Ion channels: frozen motion.

scientific article

Ion-blocking sites of the Kir2.1 channel revealed by multiscale modeling.

scientific article published in September 2009

Ion-channel gating mechanisms: model identification and parameter estimation from single channel recordings.

scientific article published in May 1989

Ion-channel properties of mastoparan, a 14-residue peptide from wasp venom, and of MP3, a 12-residue analogue ⬇️

scientific article published on April 23, 1990

Kv channel S6 helix as a molecular switch: simulation studies.

scientific article published in February 2004

Large Scale Membrane Movement Induced by a Cation Switch

preprint

Large Scale Membrane Movement Induced by a Cation Switch

working paper

Large scale model lipid membrane movement induced by a cation switch

Lipid Bilayer Membrane Perturbation by Embedded Nanopores: A Simulation Study.

scientific article published on 9 March 2016

Lipid bilayer deformation and the free energy of interaction of a Kv channel gating-modifier toxin.

scientific article published on 11 July 2008

Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations

scientific article published on 2 March 2016

Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes.

scientific article

Lipid/protein interactions and the membrane/water interfacial region

scientific article published on 01 December 2003

Lipidbook: a public repository for force-field parameters used in membrane simulations.

scientific article

Liquid-vapor oscillations of water in hydrophobic nanopores

scientific article

Local Lipid Reorganization by a Transmembrane Protein Domain.

scientific article published on 15 November 2012

Local frustration determines loop opening during the catalytic cycle of an oxidoreductase

scientific article published on 22 June 2020

Locating a plausible binding site for an open-channel blocker, GlyH-101, in the pore of the cystic fibrosis transmembrane conductance regulator.

scientific article

Louise Johnson (1940-2012).

scientific article published in October 2012

MD simulations of spontaneous membrane protein/detergent micelle formation.

scientific article

Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles.

scientific article

Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs

scientific article published on 27 July 2020

Mechanosensitive channels: stress relief.

scientific article

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes.

scientific article

Membrane Binding of Antimicrobial Peptides Is Modulated by Lipid Charge Modification

scientific article published on 04 January 2021

Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane.

scientific article published on 2 August 2016

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR

scientific article published on 15 March 2021

Membrane insertion of a voltage sensor helix

scientific article

Membrane perturbation by carbon nanotube insertion: pathways to internalization.

scientific article

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

scientific article

Membrane protein structure quality in molecular dynamics simulation.

scientific article

Membrane proteins: A tale of barrels and corks.

scientific article

Membrane proteins: Aquaporins--channels without ions.

scientific article

Membrane proteins: molecular dynamics simulations.

scientific article published on 10 April 2008

Membrane simulations: bigger and better?

scientific article

Membrane stiffness is modified by integral membrane proteins

scientific article published on September 2016

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

scientific article published on 23 September 2021

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

Membrane/Toxin Interaction Energetics via Serial Multiscale Molecular Dynamics Simulations.

scientific article

Mg 2+ -dependent conformational equilibria in CorA: an integrated view on transport regulation

Modeling Suggests TRPC3 Hydrogen Bonding and Not Phosphorylation Contributes to the Ataxia Phenotype of the Moonwalker Mouse.

scientific article

Modelling and simulation of ion channels: applications to the nicotinic acetylcholine receptor.

scientific article published in January 1998

Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices

scientific article published on 01 November 1995

Modified Bacterial Lipids Which Alter Membrane Surface Charge Reduce Binding of Antimicrobial Peptides

Modulation of A2aR Oligomerisation by Conformational State and PIP 2 Interactions Revealed by MD Simulations and Markov Models

Modulation of adenosine A2a receptor oligomerization by receptor activation and PIP<sub>2</sub> interactions

scientific article published on 15 July 2021

Molecular contacts in the transmembrane c-subunit oligomer of F-ATPases identified by tryptophan substitution mutagenesis

scientific article published on 01 July 2000

Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function.

scientific article published in March 2005

Molecular dynamics simulations and KcsA channel gating.

scientific article published on 15 March 2002

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment

scientific article published on 01 January 2005

Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei.

scientific article

Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis.

scientific article

Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study

scientific article published on 28 February 2007

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale

scientific article

Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor.

scientific article published on 2 March 2006

Molecular dynamics studies of AChBP with nicotine and carbamylcholine: the role of water in the binding pocket

scientific article published on 26 June 2007

Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms.

scientific article published in January 2008

Molecular simulation approaches to membrane proteins.

scientific article

Molecular simulation studies of hydrophobic gating in nanopores and ion channels

scientific article published on April 2015

Molecular simulations of glycolipids: Towards mammalian cell membrane models

scientific article

Monotopic enzymes and lipid bilayers: a comparative study

scientific article published on 21 February 2007

Multi-scale simulation of the simian immunodeficiency virus fusion peptide.

scientific article published on 9 November 2012

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes

scientific article published on 19 February 2020

Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes ⬇️

scientific article

Multiscale methods for macromolecular simulations.

scientific article published on 17 September 2008

Multiscale simulations of the antimicrobial peptide maculatin 1.1: water permeation through disordered aggregates.

scientific article

Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins.

scientific article published on 18 April 2013

Not Ions Alone: Barriers to Ion Permeation in Nanopores and Channels

scientific article published on 01 November 2004

OmpT: molecular dynamics simulations of an outer membrane enzyme

scientific article

On a novel rate theory for transport in narrow ion channels and its application to the study of flux optimization via geometric effects.

scientific article published in February 2009

On the interpretation of reflectivity data from lipid bilayers in terms of molecular-dynamics models. ⬇️

scientific article

Organization and Dynamics of Receptor Proteins in a Plasma Membrane

scientific article published on 30 October 2015

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.

scientific article

PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations.

scientific article published on November 2009

PX- and FYVE-mediated interactions with membranes: simulation studies.

scientific article published in June 2009

Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain

scientific article published on 03 June 2022

Peptide-bilayer interactions: simulations of dermaseptin B, an antimicrobial peptide.

scientific article published in February 1999

Poisson sampling-based inference for single ion channel data with time interval omission

scientific article published on December 22, 1992

Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations

scientific article published on 01 February 2001

Potassium channels: structures, models, simulations.

scientific article

Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: characterization via multiscale molecular dynamics simulations.

scientific article published on 8 January 2014

Proline-induced distortions of transmembrane helices.

scientific article published in November 2002

Properties of integral membrane protein structures: derivation of an implicit membrane potential.

scientific article

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes.

scientific article published on 30 November 2017

Protein-water-ion interactions in a model of the pore domain of a potassium channel: a simulation study.

scientific article

Proton currents constrain structural models of voltage sensor activation

scientific article

Putting the parts together.

scientific article

PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations

scientific article published on 12 January 2022

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

Quality Assurance for Biomolecular Simulations.

scientific article published in November 2006

Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA

scientific article

Relative Affinities of Protein–Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations

scientific article published on 15 September 2021

Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics

scientific article published on 30 August 2016

Secondary structure of an isolated P-region from the voltage-gated sodium channel: a molecular modelling/dynamics study

scientific article published on 01 December 1997

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

scientific article published on 11 July 2008

Setting up and optimization of membrane protein simulations.

scientific article

Side pockets provide the basis for a new mechanism of Kv channel-specific inhibition.

scientific article

Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices

scientific article

Simulation of the packing of idealized transmembrane alpha-helix bundles

scientific article published on 01 January 1999

Simulation of voltage-dependent interactions of alpha-helical peptides with lipid bilayers

scientific article published on 01 June 1996

Simulation-based prediction of phosphatidylinositol 4,5-bisphosphate binding to an ion channel.

scientific article

Simulations of a protein translocation pore: SecY

scientific article published on 01 October 2006

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate.

scientific article published on 04 December 2009

Simulations of the BM2 proton channel transmembrane domain from influenza virus B

scientific article published on 01 October 2009

Stability and dynamics of membrane-spanning DNA nanopores.

scientific article

Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment.

scientific article

State-Dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo -Mimetic Membranes

State-dependent network connectivity determines gating in a K+ channel

scientific article

Structural and Functional Characterization of the Kindlin-1 Pleckstrin Homology Domain

scientific article

Structural basis of Smoothened regulation by its extracellular domains

scientific article

Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies

scientific article published on 01 August 1995

Structural model for the protein-translocating element of the twin-arginine transport system

scientific article

Structure and Dynamics of Cinnamycin-Lipid Complexes: Mechanisms of Selectivity for Phosphatidylethanolamine Lipids

scientific article published on 28 October 2019

Structure and dynamics of the membrane-bound cytochrome P450 2C9

scientific article

Structure and function of natural proteins for water transport: general discussion

scientific article published on 01 September 2018

Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain ⬇️

scientific article published on 14 December 2016

Structure and orientation of the mammalian antibacterial peptide cecropin P1 within phospholipid membranes

scientific article published on 01 May 1996

Structure of a molecular hole-punch

scientific article published in Nature

Structure of the TatC core of the twin-arginine protein transport system

scientific article

Structure, mechanism, and inhibition of Hedgehog acyltransferase

scientific article published on 09 December 2021

Structure-function relationships in helix-bundle channels probed via total chemical synthesis of alamethicin dimers: effects of a Gln7 to Asn7 mutation

scientific article published on 01 November 1997

Structures of the EphA2 Receptor at the Membrane: Role of Lipid Interactions.

scientific article published on 22 December 2015

Structures of the otopetrin proton channels Otop1 and Otop3

scientific article published on 03 June 2019

Super-complexes of adhesion GPCRs and neural guidance receptors

scientific article published on 19 April 2016

Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria.

scientific article

Switching Cytolytic Nanopores into Antimicrobial Fractal Ruptures by a Single Side Chain Mutation

scientific article published on 22 April 2021

Tetrameric structure of SUR2B revealed by electron microscopy of oriented single particles

scientific journal article

The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations. ⬇️

scientific article published on 27 July 2016

The MscS-like channel YnaI has a gating mechanism based on flexible pore helices

scientific article published on 04 November 2020

The Role of C2 Domains in Two Different Phosphatases: PTEN and SHIP2

preprint

The Role of C2 Domains in Two Different Phosphatases: PTEN and SHIP2

The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope.

scientific article published on 23 January 2016

The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1.

scientific article published on 5 November 2010

The effect of mutations in the lid region of Thermomyces lanuginosus lipase on interactions with triglyceride surfaces: A multi-scale simulation study.

scientific article

The effects of stretch activation on ionic selectivity of the TREK-2 K2P K+ channel.

scientific article published on 19 July 2017

The energetics of protein-lipid interactions as viewed by molecular simulations

scientific article published on 01 February 2020

The energetics of transmembrane helix insertion into a lipid bilayer.

scientific article

The free energy landscape of dimerization of a membrane protein, NanC.

scientific article published on 9 January 2014

The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores

scientific article published on 01 June 2004

The influenza A virus M2 channel: a molecular modeling and simulation study.

scientific article published in June 1997

The interaction of C60 and its derivatives with a lipid bilayer via molecular dynamics simulations

scientific article published on 24 February 2009

The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.

scientific article published on 9 May 2008

The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating.

scientific article published on 2 December 2005

The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids

scientific article published on 17 March 2015

The modelling and enhancement of water hydrodynamics: general discussion

scientific article published on 01 September 2018

The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism

scientific article published on 23 September 2019

The pore structure and gating mechanism of K2P channels.

scientific article

The properties of ion channels formed by zervamicins

scientific article published on 01 January 1992

The role of 2-methyl-2, 4-pentanediol in sodium dodecyl sulfate micelle dissociation unveiled by dynamic light scattering and molecular dynamics simulations.

scientific article

The role of extra-membranous inter-helical loops in helix-helix interactions.

scientific article

The role of lipids in mechanosensation

scientific article

The roles of serine and threonine sidechains in ion channels: a modelling study

scientific article published on 01 January 1992

The selectivity of K+ ion channels: testing the hypotheses

scientific article published on 12 September 2008

The simulation approach to bacterial outer membrane proteins.

scientific article published on May 2004

The structural basis of ZMPSTE24-dependent laminopathies

scientific article

The structure of the HIV-1 Vpu ion channel: modelling and simulation studies.

scientific article published in June 2001

The α7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics.

scientific article published in May 2005

Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database

article

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