… 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 …

… 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. …

… 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 …

… 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. …

… 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 …

… 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 …

… 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: …

… 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 …

… 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 …

… 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 …