Long-time-step molecular dynamics through hydrogen mass repartitioning

CW Hopkins, S Le Grand, RC Walker… - Journal of chemical …, 2015 - ACS Publications
Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …

Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs

Z Li, X Li, YY Huang, Y Wu, R Liu… - Proceedings of the …, 2020 - National Acad Sciences
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for …

Biomembranes in atomistic and coarse-grained simulations

K Pluhackova, RA Böckmann - Journal of physics: condensed …, 2015 - iopscience.iop.org
The architecture of biological membranes is tightly coupled to the localization, organization,
and function of membrane proteins. The organelle-specific distribution of lipids allows for the …

Guidelines for the analysis of free energy calculations

PV Klimovich, MR Shirts, DL Mobley - Journal of computer-aided molecular …, 2015 - Springer
Free energy calculations based on molecular dynamics simulations show considerable
promise for applications ranging from drug discovery to prediction of physical properties and …

Recent H3N2 viruses have evolved specificity for extended, branched human-type receptors, conferring potential for increased avidity

W Peng, RP de Vries, OC Grant, AJ Thompson… - Cell host & …, 2017 - cell.com
Human and avian influenza viruses recognize different sialic acid-containing receptors,
referred to as human-type (NeuAcα2-6Gal) and avian-type (NeuAcα2-3Gal), respectively …

Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs)

AT Slominski, TK Kim, S Qayyum, Y Song… - Scientific Reports, 2021 - nature.com
The interactions of derivatives of lumisterol (L3) and vitamin D3 (D3) with liver X receptors
(LXRs) were investigated. Molecular docking using crystal structures of the ligand binding …

Hyaluronan/collagen hydrogels containing sulfated hyaluronan improve wound healing by sustained release of heparin-binding EGF-like growth factor

S Thönes, S Rother, T Wippold, J Blaszkiewicz… - Acta biomaterialia, 2019 - Elsevier
Functional biomaterials that are able to bind, stabilize and release bioactive proteins in a
defined manner are required for the controlled delivery of such to the desired place of action …

Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan*[S]

M Nakano, SK Mishra, Y Tokoro, K Sato… - Molecular & Cellular …, 2019 - ASBMB
Glycoproteins are decorated with complex glycans for protein functions. However, regulation
mechanisms of complex glycan biosynthesis are largely unclear. Here we found that …

Vaccinomics to Design a Multi-Epitopes Vaccine for Acinetobacter baumannii

M Ud-Din, A Albutti, A Ullah, S Ismail, S Ahmad… - International Journal of …, 2022 - mdpi.com
Antibiotic resistance (AR) is the result of microbes' natural evolution to withstand the action
of antibiotics used against them. AR is rising to a high level across the globe, and novel …

Designing of a Recombinant Multi-Epitopes Based Vaccine against Enterococcus mundtii Using Bioinformatics and Immunoinformatics Approaches

M Alharbi, A Alshammari, AF Alasmari… - International journal of …, 2022 - mdpi.com
Enterococcus species are an emerging group of bacterial pathogens that have a significant
role in hospital-associated infections and are associated with higher mortality and morbidity …