Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

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 Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

SJ Park, J Lee, Y Qi, NR Kern, HS Lee, S Jo… - …, 2019 - academic.oup.com
Characterizing glycans and glycoconjugates in the context of three-dimensional structures is
important in understanding their biological roles and developing efficient therapeutic agents …

Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities

L Casalino, C Seitz, J Lederhofer… - ACS Central …, 2022 - ACS Publications
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-
19 pandemic, raising serious concerns about the nature and magnitude of future epidemics …

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

F Grünewald, R Alessandri, PC Kroon… - Nature …, 2022 - nature.com
Molecular dynamics simulations play an increasingly important role in the rational design of
(nano)-materials and in the study of biomacromolecules. However, generating input files …

Martinize2 and vermouth: Unified framework for topology generation

PC Kroon, F Grünewald, J Barnoud… - arXiv preprint arXiv …, 2022 - arxiv.org
Ongoing advances in force field and computer hardware development enable the use of
molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of …

Recent development of boronic acid-based fluorescent sensors

G Fang, H Wang, Z Bian, J Sun, A Liu, H Fang, B Liu… - RSC …, 2018 - pubs.rsc.org
As Lewis acids, boronic acids can bind with 1, 2-or 1, 3-diols in aqueous solution reversibly
and covalently to form five or six cyclic esters, thus resulting in significant fluorescence …

Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain

T Gutmann, IB Schäfer, C Poojari, B Brankatschk… - Journal of Cell …, 2019 - rupress.org
Glucose homeostasis and growth essentially depend on the hormone insulin engaging its
receptor. Despite biochemical and structural advances, a fundamental contradiction has …

Lignocellulosic biomass-based glycoconjugates for diverse biotechnological applications

CER Reis, TS Milessi, MDN Ramos, AK Singh… - Biotechnology …, 2023 - Elsevier
Glycoconjugates are the ubiquitous components of mammalian cells, mainly synthesized by
covalent bonds of carbohydrates to other biomolecules such as proteins and lipids, with a …