Diffdock: Diffusion steps, twists, and turns for molecular docking
… generative model (DGM) over the space of ligand poses for molecular docking. We define
a diffusion process over the degrees of freedom involved in docking: the position of the ligand …
a diffusion process over the degrees of freedom involved in docking: the position of the ligand …
Diffusion models in protein structure and docking
… generation and small molecule docking. This review covers the basics of diffusion models, …
(4 and 5) We repeat Steps 1–3 multiple times to simulate a SDE trajectory on the manifold. …
(4 and 5) We repeat Steps 1–3 multiple times to simulate a SDE trajectory on the manifold. …
[PDF][PDF] FusionDock: physics-informed diffusion model for molecular docking
MR Masters, AH Mahmoud… - ICML workshop on …, 2023 - icml-compbio.github.io
… a diffusion model for protein-ligand docking which incorporates physical priors, such as
classical mechanics principles, known molecular … once at each time step, the repulsive force can …
classical mechanics principles, known molecular … once at each time step, the repulsive force can …
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge
… docking to predict poses of ligand and pocket sidechains simultaneously and introduce
Re-Dock, a novel diffusion … Further, we achieve better results than diffusion with fewer time steps. …
Re-Dock, a novel diffusion … Further, we achieve better results than diffusion with fewer time steps. …
[HTML][HTML] Single-molecule fluorescence studies of a PH domain: new insights into the membrane docking reaction
… the first to use single-molecule TIRFM with purified protein and synthetic bilayers to investigate
the molecular mechanisms of a membrane targeting domain docking to, diffusing on, and …
the molecular mechanisms of a membrane targeting domain docking to, diffusing on, and …
Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin
Z Zhang, Y Goldtzvik… - Proceedings of the …, 2017 - National Acad Sciences
… On the other hand, if a majority of the 16-nm step is covered by diffusion of the TH, we expect
the motion of the TH to be bidirectional, and the extent of stochastic random walk of the TH …
the motion of the TH to be bidirectional, and the extent of stochastic random walk of the TH …
Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets
T Voitsitskyi, V Bdzhola, R Stratiichuk, I Koleiev… - RSC …, 2024 - pubs.rsc.org
… PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule
poses … For each of the 13 interactions listed in Table 1, the following steps are performed: …
poses … For each of the 13 interactions listed in Table 1, the following steps are performed: …
Kinetics of docking in postnucleation stages of self-assembly
RA Garza-López, P Bouchard, G Nicolis… - The Journal of …, 2008 - pubs.aip.org
… in which docking is principally controlled by surface diffusion … by a “direct hit” docking
event. The theoretical implications of … step, thus partitioning the surface available to a diffusing …
event. The theoretical implications of … step, thus partitioning the surface available to a diffusing …
DiffSim: Aligning Diffusion Model and Molecular Dynamics Simulation for Accurate Blind Docking
Y Fei, Y Li, Z Zhou, H Wang - openreview.net
… Specifically, molecular docking is used as an initial step to predict several possible binding
poses and rank them based on binding affinities. The top-ranked protein-ligand complexes …
poses and rank them based on binding affinities. The top-ranked protein-ligand complexes …
[HTML][HTML] Deep confident steps to new pockets: Strategies for docking generalization
… early diffusion steps by changing the weights of the score model. The pink regions of the
protein represent areas to where the docking … of bootstrapping, the diffusion model is pushed to …
protein represent areas to where the docking … of bootstrapping, the diffusion model is pushed to …
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