Related papers: Harmonic Self-Conditioned Flow Matching for Multi-…

Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem…

Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…

Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…

Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle…

With the aim to parallelize and monitor biological or biochemical phenomena, trapping and immobilization of objects such as particles, droplets or cells in microfluidic devices has been an intense area of research and engineering so far.…

Recently, Flow Matching models have pushed the boundaries of high-fidelity data generation across a wide range of domains. It typically employs a single large network to learn the entire generative trajectory from noise to data. Despite…

Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…

The scarcity of experimental protein-ligand complexes poses a significant challenge for training robust deep learning models for molecular docking. Given the prohibitive cost and time constraints associated with experimental structure…

Flow matching has emerged as a simulation-free alternative to diffusion-based generative modeling, producing samples by solving an ODE whose time-dependent velocity field is learned along an interpolation between a simple source…

Flow matching is a recent framework to train generative models that exhibits impressive empirical performance while being relatively easier to train compared with diffusion-based models. Despite its advantageous properties, prior methods…

Flow matching has recently emerged as a powerful alternative to diffusion models, providing a continuous-time formulation for generative modeling and representation learning. Yet, we show that this framework suffers from a fundamental…

Recovering 3D human poses from a monocular camera view is a highly ill-posed problem due to the depth ambiguity. Earlier studies on 3D human pose lifting from 2D often contain incorrect-yet-overconfident 3D estimations. To mitigate the…

To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first…

Predicting low-energy molecular conformations given a molecular graph is an important but challenging task in computational drug discovery. Existing state-of-the-art approaches either resort to large scale transformer-based models that…

Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing challenges for…

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…

Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…