[HTML][HTML] Advancements in molecular simulation for understanding pharmaceutical pollutant Adsorption: A State-of-the-Art review

I Salahshoori, S Mahdavi, Z Moradi, M Otadi… - Journal of Molecular …, 2024‏ - Elsevier
The contamination of natural water resources by pharmaceutical pollutants has become a
significant environmental concern. Traditional experimental approaches for understanding …

NGL Viewer: a web application for molecular visualization

AS Rose, PW Hildebrand - Nucleic acids research, 2015‏ - academic.oup.com
Abstract The NGL Viewer (http://proteinformatics. charite. de/ngl) is a web application for the
visualization of macromolecular structures. By fully adopting capabilities of modern web …

Molecular graphics: bridging structural biologists and computer scientists

X Martinez, M Krone, N Alharbi, AS Rose, RS Laramee… - Structure, 2019‏ - cell.com
Visualization of molecular structures is one of the most common tasks carried out by
structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In …

Shortcuts for faster image creation in PyMOL

BHM Mooers - Protein Science, 2020‏ - Wiley Online Library
PyMOL is often used to generate images of biomolecular structures. Hundreds of
parameters in PyMOL provide precise control over the appearance of structures. We …

Phosphatidic acid counteracts S-RNase signaling in pollen by stabilizing the actin cytoskeleton

J Chen, P Wang, BHJ De Graaf, H Zhang, H Jiao… - The Plant …, 2018‏ - academic.oup.com
S-RNase is the female determinant of self-incompatibility (SI) in pear (Pyrus bretschneideri).
After translocation to the pollen tube, S-RNase degrades rRNA and induces pollen tube …

Templates for writing PyMOL scripts

BHM Mooers, ME Brown - Protein Science, 2021‏ - Wiley Online Library
PyMOL commands are used to exert exquisite control over the appearance of a molecular
model. This control has made PyMOL popular for making images of protein structures for …

Comprehensive in silico analyses of flavonoids elucidating the drug properties against kidney disease by targeting AIM2

M Kandeel, MN Iqbal, I Ali, S Malik, A Malik… - PLoS One, 2023‏ - journals.plos.org
Kidney disorders are among the most common diseases and there is a scarcity of effective
treatments for chronic kidney disease. There has been a progressive improvement in …

Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models

P Larsson, PM Kasson - PLoS Computational Biology, 2013‏ - journals.plos.org
Fusion peptides from influenza hemagglutinin act on membranes to promote membrane
fusion, but the mechanism by which they do so remains unknown. Recent theoretical work …

An introduction to programming for bioscientists: a Python-based primer

B Ekmekci, CE McAnany, C Mura - PLoS computational biology, 2016‏ - journals.plos.org
Computing has revolutionized the biological sciences over the past several decades, such
that virtually all contemporary research in molecular biology, biochemistry, and other …

PlayMolecule Viewer: a toolkit for the visualization of molecules and other data

M Torrens-Fontanals, P Tourlas, S Doerr… - Journal of Chemical …, 2024‏ - ACS Publications
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the
exploration of data resulting from structural bioinformatics or computer-aided drug design …