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

Pylipid: A Python Toolkit for Analysis of Lipid-Protein Interactions from MD Simulations

(2021) Wanling Song et al.   BIOPHYSICAL JOURNAL

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

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

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

(2019) Giray Enkavi et al.   CHEMICAL REVIEWS

Emerging Diversity in Lipid–Protein Interactions

(2019) Valentina Corradi et al.   CHEMICAL REVIEWS

Smoothened stimulation by membrane sterols drives Hedgehog pathway activity

(2019) Ishan Deshpande et al.   NATURE

NGL viewer: web-based molecular graphics for large complexes

(2018) Alexander S Rose et al.   BIOINFORMATICS

Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins

(2018) Valentina Corradi et al.   ACS Central Science

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

(2018) Hsin-Yung Yen et al.   NATURE

Structural basis of Smoothened regulation by its extracellular domains

(2016) Eamon F. X. Byrne et al.   NATURE

Cholesterol activates the G-protein coupled receptor Smoothened to promote Hedgehog signaling

(2016) Giovanni Luchetti et al.   eLife

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

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

NGL Viewer: a web application for molecular visualization

(2015) Alexander S. Rose et al.   NUCLEIC ACIDS RESEARCH

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

(2014) Julien C Thibault et al.   Journal of Cheminformatics

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY