CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

S Feng, S Park, YK Choi, W Im - Journal of chemical theory and …, 2023 - ACS Publications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …

[HTML][HTML] Lipid interaction sites on channels, transporters and receptors: recent insights from molecular dynamics simulations

G Hedger, MSP Sansom - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Lipid molecules are able to selectively interact with specific sites on integral membrane
proteins, and modulate their structure and function. Identification and characterization of …

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

J Lee, DS Patel, J Ståhle, SJ Park… - Journal of chemical …, 2018 - ACS Publications
Glycolipids (such as glycoglycerolipids, glycosphingolipids, and
glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS) …

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

EL Wu, X Cheng, S Jo, H Rui, KC Song… - 2014 - Wiley Online Library
CHARMM‐GUI Membrane Builder, http://www. charmm‐gui. org/input/membrane, is a web‐
based user interface designed to interactively build all‐atom protein/membrane or …

OPM database and PPM web server: resources for positioning of proteins in membranes

MA Lomize, ID Pogozheva, H Joo… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Orientations of Proteins in Membranes (OPM) database is a curated web
resource that provides spatial positions of membrane-bound peptides and proteins of known …

[HTML][HTML] Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review

M Deleu, JM Crowet, MN Nasir, L Lins - Biochimica et Biophysica Acta (BBA …, 2014 - Elsevier
Plasma membranes are complex entities common to all living cells. The basic principle of
their organization appears very simple, but they are actually of high complexity and …

APL@ Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories

G Lukat, J Krüger, B Sommer - Journal of chemical information …, 2013 - ACS Publications
APL@ Voro is a new program developed to aid in the analysis of GROMACS trajectories of
lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a …

Preparation, characterization, cytotoxicity and pharmacokinetics of niosomes containing gemcitabine: In vitro, in vivo, and simulation studies

M Barani, MR Ha**ezhad, F Zargari, S Shahraki… - Journal of Drug Delivery …, 2023 - Elsevier
Novel niosomes including cholesterol, Span (60), Tween (60), and gemcitabine (GEM) have
been developed via film hydration approach and characterized via in vitro, in vivo, and in …

Polymyxins Bind to the Cell Surface of Unculturable Acinetobacter baumannii and Cause Unique Dependent Resistance

Y Zhu, J Lu, ML Han, X Jiang, MAK Azad… - Advanced …, 2020 - Wiley Online Library
Multidrug‐resistant Acinetobacter baumannii is a top‐priority pathogen globally and
polymyxins are a last‐line therapy. Polymyxin dependence in A. baumannii (ie …

[HTML][HTML] Simulation, in vitro, and in vivo cytotoxicity assessments of methotrexate-loaded pH-responsive nanocarriers

M Barani, M Reza Ha**ezhad, S Sargazi, M Zeeshan… - Polymers, 2021 - mdpi.com
In this study, pH-responsive niosomal methotrexate (MTX) modified with ergosterol was
prepared for potential anticancer application. The prepared formulation had a size of …