Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies

Y Yamazaki, N Zhao, TR Caulfield, CC Liu… - Nature Reviews …, 2019 - nature.com
Polymorphism in the apolipoprotein E (APOE) gene is a major genetic risk determinant of
late-onset Alzheimer disease (AD), with the APOE* ε 4 allele conferring an increased risk …

Homology modeling in drug discovery: Overview, current applications, and future perspectives

MT Muhammed, E Aki‐Yalcin - Chemical biology & drug design, 2019 - Wiley Online Library
Homology modeling is one of the computational structure prediction methods that are used
to determine protein 3D structure from its amino acid sequence. It is considered to be the …

Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study

AA Elfiky - Life sciences, 2020 - Elsevier
Aims A new human coronavirus (HCoV), which has been designated SARS-CoV-2, began
spreading in December 2019 in Wuhan City, China causing pneumonia called COVID-19 …

Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

AA Elfiky - Life sciences, 2020 - Elsevier
Aims A newly emerged Human Coronavirus (HCoV) is reported two months ago in Wuhan,
China (COVID-19). Until today> 2700 deaths from the 80,000 confirmed cases reported …

SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective

AA Elfiky - Journal of Biomolecular Structure and Dynamics, 2021 - Taylor & Francis
New treatment against SARS-CoV-2 now is a must. Nowadays, the world encounters a huge
health crisis by the COVID-19 viral infection. Nucleotide inhibitors gave a lot of promising …

[PDF][PDF] ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

TI Croll - Acta Crystallographica Section D: Structural Biology, 2018 - journals.iucr.org
This paper introduces ISOLDE, a new software package designed to provide an intuitive
environment for high-fidelity interactive remodelling/refinement of macromolecular models …

YASARA: a tool to obtain structural guidance in biocatalytic investigations

H Land, MS Humble - Protein engineering: methods and protocols, 2018 - Springer
In biocatalysis, structural knowledge regarding an enzyme and its substrate interactions
complements and guides experimental investigations. Structural knowledge regarding an …

Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery

TS Lee, BK Allen, TJ Giese, Z Guo, P Li… - Journal of Chemical …, 2020 - ACS Publications
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

[HTML][HTML] A guide to in silico drug design

Y Chang, BA Hawkins, JJ Du, PW Groundwater… - Pharmaceutics, 2023 - mdpi.com
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …

[PDF][PDF] The PDB_REDO server for macromolecular structure model optimization

RP Joosten, F Long, GN Murshudov, A Perrakis - IUCrJ, 2014 - journals.iucr.org
The refinement and validation of a crystallographic structure model is the last step before the
coordinates and the associated data are submitted to the Protein Data Bank (PDB). The …