Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

E Yuriev, J Holien, PA Ramsland - Journal of Molecular …, 2015 - Wiley Online Library
Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …

Force field optimization guided by small molecule crystal lattice data enables consistent sub-angstrom protein–ligand docking

H Park, G Zhou, M Baek, D Baker… - Journal of Chemical …, 2021 - ACS Publications
Accurate and rapid calculation of protein-small molecule interaction free energies is critical
for computational drug discovery. Because of the large chemical space spanned by drug …

In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against …

M Aamir, VK Singh, MK Dubey, M Meena… - Frontiers in …, 2018 - frontiersin.org
Vascular wilt of tomato caused by Fusarium oxysporum f. sp. lycopersici (FOL) is one of the
most devastating diseases, that delimits the tomato production worldwide. Fungal short …

Borneol ester derivatives as entry inhibitors of a wide spectrum of SARS-CoV-2 viruses

OI Yarovaya, DN Shcherbakov, SS Borisevich… - Viruses, 2022 - mdpi.com
In the present work we studied the antiviral activity of the home library of monoterpenoid
derivatives using the pseudoviral systems of our development, which have glycoproteins of …

Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions

DD Wang, M Zhu, H Yan - Briefings in bioinformatics, 2021 - academic.oup.com
Accurately predicting protein–ligand binding affinities can substantially facilitate the drug
discovery process, but it remains as a difficult problem. To tackle the challenge, many …

Naphthyl-Substituted Indole and Pyrrole Carboxylic Acids as Effective Antibiotic Potentiators—Inhibitors of Bacterial Cystathionine γ-Lyase

AS Kuzovlev, MD Zybalov, AV Golovin… - International Journal of …, 2023 - mdpi.com
Over the past decades, the problem of bacterial resistance to most antibiotics has become a
serious threat to patients' survival. Nevertheless, antibiotics of a novel class have not been …

[HTML][HTML] Immunoinformatics approach to designing a multi-epitope vaccine against Saint Louis Encephalitis Virus

MS Hossain, MI Hossan, S Mizan, AT Moin… - Informatics in Medicine …, 2021 - Elsevier
Abstract The Saint Louis Encephalitis Virus (SLEV) is one of the causes of a rare,
inflammatory condition of the brain tissues known as encephalitis. Belonging to the …

Usnic acid based thiazole-hydrazones as multi-targeting inhibitors of a wide spectrum of SARS-CoV-2 viruses

OI Yarovaya, AS Filimonov, DS Baev… - New Journal of …, 2023 - pubs.rsc.org
Although the Covid-19 pandemic is officially over and the spread of coronavirus infection is
no longer considered an international emergency, the virus continues to persist in the …

Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of Staphylococcus aureus

B Ramachandran, V Srinivasadesikan… - Journal of …, 2022 - Taylor & Francis
The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The
flavonoid derivatives possess various biological activities such as antimicrobial, anti …

Induction of apoptosis by pyrazolo [3, 4-d] pyridazine derivative in lung cancer cells via disruption of Bcl-2/Bax expression balance

MS Mohamed, AO Abdelhamid, FM Almutairi… - Bioorganic & medicinal …, 2018 - Elsevier
In the rapidly expanding era of cancer target therapy, regulators of apoptosis are emerging
as attractive therapeutic targets. X-linked inhibitor of apoptosis (XIAP) is of specific interest …