SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

M Bugnon, UF Röhrig, M Goullieux… - Nucleic Acids …, 2024 - academic.oup.com
Drug discovery aims to identify potential therapeutic compounds capable of modulating the
activity of specific biological targets. Molecular docking can efficiently support this process …

Elucidating governing factors of PFAS removal by polyamide membranes using machine learning and molecular simulations

N Jeong, S Park, S Mahajan, J Zhou… - Nature …, 2024 - nature.com
Per-and polyfluoroalkyl substances (PFASs) have recently garnered considerable concerns
regarding their impacts on human and ecological health. Despite the important roles of …

Combinatory Effect of Gemcitabine and 5‐Fluorouracil Investigated Through Chemoinformatics and Molecular Dynamics Simulation Against Breast Cancer

S Sukumaran, A Zochedh, K Chandran… - … Journal of Quantum …, 2024 - Wiley Online Library
Co‐delivering FDA‐approved drugs can be less harmful and boost biological activity by
targeting different protein mechanism at same time. Gemcitabine and 5‐Fluorouracil (GE5F) …

Computational Assessment of the Phytochemicals of Panax ginseng CA Meyer Against Dopamine Receptor D1 for Early Huntington's Disease Prophylactics

JA Subin, RLS Shrestha - Cell Biochemistry and Biophysics, 2024 - Springer
A herb, Panax ginseng CA Meyer has been used traditionally for the treatment of various
diseases. In this work, its chemical components have been explored by computational …

[HTML][HTML] Solvation effects, structural, vibrational analysis, chemical reactivity, nanocages, ELF, LOL, docking and MD simulation on Sitagliptin

G Venkatesh, S Haseena, P Vennila… - Chemical Physics …, 2024 - Elsevier
Sitagliptin is a medication used to manage type-2 diabetes. The present study investigates
the experimental and theoretical results of Sitagliptin (SG). Density functional theory (DFT) …

Marine natural compounds as potential CBP bromodomain inhibitors for treating cancer: an in-silico approach using molecular docking, ADMET, molecular dynamics …

ML Ali, F Noushin, E Azme, MM Hasan, N Hoque… - In Silico …, 2024 - Springer
The cAMP-responsive element binding protein (CREB) binding protein (CBP), a
bromodomain-containing protein, engages with multiple transcription factors and enhances …

Amyloid accelerator polyphosphate fits as the mystery density in α-synuclein fibrils

P Huettemann, P Mahadevan, J Lempart, E Tse… - Plos …, 2024 - journals.plos.org
Aberrant aggregation of α-Synuclein is the pathological hallmark of a set of
neurodegenerative diseases termed synucleinopathies. Recent advances in cryo-electron …

Two-step covalent docking with attracting cavities

M Goullieux, V Zoete, UF Röhrig - Journal of Chemical …, 2023 - ACS Publications
Due to their various advantages, interest in the development of covalent drugs has been
renewed in the past few years. It is therefore important to accurately describe and predict …

Benchmarking forcefields for molecular dynamics simulations of polyamide-based reverse-osmosis membranes

S Mahajan, EMV Hoek, JR McCutcheon, Y Li - Journal of Membrane …, 2025 - Elsevier
Molecular dynamics simulations offer unique insights about solvent and solute transport
through the active layer of reverse-osmosis membranes at sub-nanometer to nanometer …

Kinetic and in silico structural characterization of norbelladine O-methyltransferase of Amaryllidaceae alkaloids biosynthesis

M Koirala, N Merindol, V Karimzadegan… - Journal of Biological …, 2024 - jbc.org
Amaryllidaceae alkaloids are a diverse group of alkaloids exclusively reported from the
Amaryllidaceae plant family. In planta, their biosynthesis is still not fully characterized; …