De novo design of anti-COVID drugs using machine learning-based equivariant diffusion model targeting the spike protein

V Niranjan, A Uttarkar, A Ramakrishnan… - … Issues in Molecular …, 2023 - mdpi.com
… In modern drug discovery, molecular docking methods are used to explore the complexes
formed … was combined with a forward representation of the pocket in each denoising step [12]. …

A 20-nm step toward the cell membrane preceding exocytosis may correspond to docking of tethered granules

E Karatekin, VS Tran, S Huet, I Fanget, S Cribier… - Biophysical journal, 2008 - cell.com
… We propose that such a step originates when a cell-membrane-attached vesicle
undergoes a transition from the tethered to the docked state in preparation for exocytosis. …

Antimicrobial activity of ginger on cariogenic bacteria: molecular networking and molecular docking analyses

L Babaeekhou, M Ghane - Journal of Biomolecular Structure and …, 2021 - Taylor & Francis
… Agar well diffusion method was applied to … Docking analysis can also be done on molecules
responsible for human disorders like dementia or cancer. The second step after docking

Equivariant 3D-conditional diffusion model for molecular linker design

I Igashov, H Stärk, C Vignac, A Schneuing… - Nature Machine …, 2024 - nature.com
… employ valency rules at each generation step, while our model is shown to … molecules were
minimized using the molecular docking software GNINA 19 . We report the resulting docking

… assessed using single-molecule-detection fluorescence correlation spectroscopy, laser-scanning microscopy, transmission electron microscopy, and in silico docking

S Hossain, M Hashimoto, M Katakura… - … and alternative medicine, 2015 - Springer
… the Brownian diffusion times of moving particles in a small confocal volume at the single-molecule
level, was used. If asiaticoside inhibits early Aβ 1–42 fibrillation steps, more Aβs …

NMR‐Assisted Molecular Docking Methodologies

M Sturlese, M Bellanda, S Moro - Molecular Informatics, 2015 - Wiley Online Library
… efficiently transferred also to the ligand through spin diffusion, resulting in the reduction of its
… In these cases, CSP data are taken into account only in the scoring step after the generation …

Two for one: Diffusion models and force fields for coarse-grained molecular dynamics

M Arts, V Garcia Satorras, CW Huang… - Journal of Chemical …, 2023 - ACS Publications
… a probability distribution by approximating the inverse of a diffusion process, ie, a denoising
process. The diffusion (forward) process is defined as a Markov chain of L steps q ( z 1 : L | z …

Virtual screening, ADMET profiling, molecular docking and dynamics approaches to search for potent selective natural molecules based inhibitors against …

S Roy, A Kumar, MH Baig, M Masařík, I Provazník - Methods, 2015 - Elsevier
Molecular docking and simulations of top hit molecules were performed to study complex
stability. … Molecular dynamics studies were performed to validate our findings. …

Efficient antibacterial/antifungal activities: Synthesis, molecular docking, molecular dynamics, pharmacokinetic, and binding free energy of galactopyranoside …

F Ahmmed, AU Islam, YE Mukhrish, YE Bakri, S Ahmad… - Molecules, 2022 - mdpi.com
… To determine MIC and MBC based on antimicrobial results, disk diffusion and broth …
the steepest descent and conjugate gradient steps for 1000 steps in each algorithm. For …

Quantum molecular docking with quantum-inspired algorithm

Y Li, X Cui, Z Xiong, B Liu, BY Wang, R Shu… - arXiv preprint arXiv …, 2024 - arxiv.org
… is based on a diffusion generative model, which defines a diffusion process transforming the
data … The step sizes of rotation angles and torsion angles are ∆ϕ = ∆θ = 2π/d. In general, the …