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

Activation of G-protein coupled receptors is thermodynamically linked to lipid solvation

(2021) Alison N. Leonard et al.   BIOPHYSICAL JOURNAL

Martini 3: a general purpose force field for coarse-grained molecular dynamics

(2021) Paulo C. T. Souza et al.   NATURE METHODS

Predictable cholesterol binding sites in GPCRs lack consensus motifs

(2021) Geoffrey J. Taghon et al.   STRUCTURE

LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations

(2021) Paul Smith et al.   Journal of Chemical Theory and Computation

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

(2021) T. Bertie Ansell et al.   Journal of Chemical Theory and Computation

CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations

(2021) Owen N. Vickery et al.   Journal of Chemical Theory and Computation

ProLint: a web-based framework for the automated data analysis and visualization of lipid–protein interactions

(2021) Besian I Sejdiu et al.   NUCLEIC ACIDS RESEARCH

Regulation of EGFR activation and signaling by lipids on the plasma membrane

(2021) Do-Hyeon Kim et al.   PROGRESS IN LIPID RESEARCH

Allosteric modulation of ghrelin receptor signaling by lipids

(2021) Marjorie Damian et al.   Nature Communications

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

(2021) Robin A. Corey et al.   Science Advances

Lipid-Protein Interactions Are a Unique Property and Defining Feature of G Protein-Coupled Receptors

(2020) Besian I. Sejdiu et al.   BIOPHYSICAL JOURNAL

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

(2020) Anna L. Duncan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein–ligand binding with the coarse-grained Martini model

(2020) Paulo C. T. Souza et al.   Nature Communications

Single-particle cryo-EM at atomic resolution

(2020) Takanori Nakane et al.   NATURE

The Unconventional Cytoplasmic Sensing Mechanism for Ethanol Chemotaxis in Bacillus subtilis

(2020) Payman Tohidifar et al.   mBio

Computational Modeling of Realistic Cell Membranes

(2019) Siewert J. Marrink et al.   CHEMICAL REVIEWS

Emerging Diversity in Lipid–Protein Interactions

(2019) Valentina Corradi et al.   CHEMICAL REVIEWS

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

(2019) Alison N. Leonard et al.   CHEMICAL REVIEWS

Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes

(2019) Moutusi Manna et al.   Annual Review of Biophysics

Tools for Understanding Nanoscale Lipid Regulation of Ion Channels

(2019) Carol V. Robinson et al.   TRENDS IN BIOCHEMICAL SCIENCES

Lipid-Dependent Regulation of Ion Channels and G Protein–Coupled Receptors: Insights from Structures and Simulations

(2019) Anna L. Duncan et al.   Annual Review of Pharmacology and Toxicology

Insights into Membrane Protein–Lipid Interactions from Free Energy Calculations

(2019) Robin A. Corey et al.   Journal of Chemical Theory and Computation

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

(2019) Robin A. Corey et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2

(2019) Qinrui Wang et al.   STRUCTURE

A Database of Predicted Binding Sites for Cholesterol on Membrane Proteins, Deep in the Membrane

(2018) Anthony G. Lee   BIOPHYSICAL JOURNAL

Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions

(2018) Leslie A. Salas-Estrada et al.   BIOPHYSICAL JOURNAL

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

(2018) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

Understanding the diversity of membrane lipid composition

(2018) Takeshi Harayama et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules

(2018) Nicolas Barbera et al.   BIOPHYSICAL JOURNAL

PtdIns(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling

(2018) Hsin-Yung Yen et al.   NATURE

A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol

(2018) Reza Salari et al.   Journal of Chemical Theory and Computation

Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer

(2018) Duncan Laverty et al.   NATURE

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

(2018) Thomas D Newport et al.   NUCLEIC ACIDS RESEARCH

Cholesterol Interaction Sites on the Transmembrane Domain of the Hedgehog Signal Transducer and Class F G Protein-Coupled Receptor Smoothened

(2018) George Hedger et al.   STRUCTURE

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

(2018) Wanling Song et al.   STRUCTURE

Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations

(2017) Albert C. Pan et al.   Journal of Chemical Theory and Computation

The role of interfacial lipids in stabilizing membrane protein oligomers

(2017) Kallol Gupta et al.   NATURE

The mystery of membrane organization: composition, regulation and roles of lipid rafts

(2017) Erdinc Sezgin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2016) George Hedger et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

FATSLiM: a fast and robust software to analyze MD simulations of membranes

(2016) Sébastien Buchoux   BIOINFORMATICS

Functional Modulation of a G Protein-Coupled Receptor Conformational Landscape in a Lipid Bilayer

(2016) Marina Casiraghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

(2016) Moutusi Manna et al.   eLife

The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations

(2015) Julie Grouleff et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

CG2AA: backmapping protein coarse-grained structures

(2015) Leandro E. Lombardi et al.   BIOINFORMATICS

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Allosteric regulation of G protein–coupled receptor activity by phospholipids

(2015) Rosie Dawaliby et al.   Nature Chemical Biology

Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

(2014) Tod D. Romo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc1

(2013) Clement Arnarez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Predictions for Cholesterol Interaction Sites on the A2A Adenosine Receptor

(2012) Ji Young Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of lipids in defining membrane protein interactions: insights from mass spectrometry

(2012) Nelson P. Barrera et al.   TRENDS IN CELL BIOLOGY

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

(2011) Phillip J. Stansfeld et al.   Journal of Chemical Theory and Computation

Raft domains of variable properties and compositions in plasma membrane vesicles

(2011) I. Levental et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Membranes: The Lipid Perspective

(2011) Ünal Coskun et al.   STRUCTURE

Mapping the Druggable Allosteric Space of G-Protein Coupled Receptors: a Fragment-Based Molecular Dynamics Approach

(2010) Anthony Ivetac et al.   Chemical Biology & Drug Design

Reconstruction of atomistic details from coarse-grained structures

(2010) Andrzej J. Rzepiela et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

PIP2 Is a Necessary Cofactor for Ion Channel Function: How and Why?

(2008) Byung-Chang Suh et al.   Annual Review of Biophysics

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations

(2008) George Khelashvili et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS