We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from a statistical model, with each option unlocking new capabilities. Hand-specifying ellipsoids enables users to control the location, size, orientation, secondary structure, and approximate shape of protein substructures. Conditioning on ellipsoids of existing proteins enables redesigning their substructure's connectivity or editing substructure properties. By conditioning on novel and diverse ellipsoid layouts from a simple statistical model, we improve protein generation with expanded Pareto frontiers between designability, novelty, and diversity. Further, this enables sampling designable proteins with a helix-fraction that matches PDB proteins, unlike existing generative models that commonly oversample conceptually simple helix bundles. Code is available at https://github.com/NVlabs/protcomposer.

Engineering molecules to exhibit precise 3D intermolecular interactions with their environment forms the basis of chemical design. In ligand-based drug design, bioisosteric analogues of known bioactive hits are often identified by virtually screening chemical libraries with shape, electrostatic, and pharmacophore similarity scoring functions. We instead hypothesize that a generative model which learns the joint distribution over 3D molecular structures and their interaction profiles may facilitate 3D interaction-aware chemical design. We specifically design ShEPhERD, an SE(3)-equivariant diffusion model which jointly diffuses/denoises 3D molecular graphs and representations of their shapes, electrostatic potential surfaces, and (directional) pharmacophores to/from Gaussian noise. Inspired by traditional ligand discovery, we compose 3D similarity scoring functions to assess ShEPhERD’s ability to conditionally generate novel molecules with desired interaction profiles. We demonstrate ShEPhERD’s potential for impact via exemplary drug design tasks including natural product ligand hopping, protein-blind bioactive hit diversification, and bioisosteric fragment merging.

Supervised machine learning techniques are increasingly being adopted to speed up electronic structure predictions, serving as alternatives to first-principles methods like Density Functional Theory (DFT). Although current DFT datasets mainly emphasize chemical properties and atomic forces, the precise prediction of electronic charge density is essential for accurately determining a system's total energy and ground state properties. In this study, we introduce a novel electronic charge density dataset named ECD, which encompasses 140,646 stable crystal geometries with medium-precision Perdew–Burke–Ernzerhof (PBE) functional data. Within this dataset, a subset of 7,147 geometries includes high-precision electronic charge density data calculated using the Heyd–Scuseria–Ernzerhof (HSE) functional in DFT. By designing various benchmark tasks for crystalline materials and emphasizing training with large-scale PBE data while fine-tuning with a smaller subset of high-precision HSE data, we demonstrate the efficacy of current machine learning models in predicting electronic charge densities.The ECD dataset and baseline models are open-sourced to support community efforts in developing new methodologies and accelerating materials design and applications.

Drug-target binding affinity prediction is a fundamental task for drug discovery. It has been extensively explored in literature and promising results are reported. However, in this paper, we demonstrate that the results may be misleading and cannot be well generalized to real practice. The core observation is that the canonical randomized split of a test set in conventional evaluation leaves the test set dominated by samples with high similarity to the training set. The performance of models is severely degraded on samples with lower similarity to the training set but the drawback is highly overlooked in current evaluation. As a result, the performance can hardly be trusted when the model meets low-similarity samples in real practice. To address this problem, we propose a framework of similarity aware evaluation in which a novel split methodology is proposed to adapt to any desired distribution. This is achieved by a formulation of optimization problems which are approximately and efficiently solved by gradient descent. We perform extensive experiments across five representative methods in four datasets for two typical target evaluations and compare them with various counterpart methods. Results demonstrate that the proposed split methodology can significantly better fit desired distributions and guide the development of models.

Understanding the physical world is a fundamental challenge in embodied AI, critical for enabling agents to perform complex tasks and operate safely in real-world environments. While Vision-Language Models (VLMs) have shown great promise in reasoning and task planning for embodied agents, their ability to comprehend physical phenomena remains extremely limited.To close this gap, we introduce PhysBench, a comprehensive benchmark designed to evaluate VLMs' physical world understanding capability across a diverse set of tasks. PhysBench contains 10,002 entries of interleaved video-image-text data, categorized into four major domains: physical object properties, physical object relationships, physical scene understanding, and physics-based dynamics, further divided into 19 subclasses and 8 distinct capability dimensions.Our extensive experiments, conducted on 75 representative VLMs, reveal that while these models excel in common-sense reasoning, they struggle with understanding the physical world---likely due to the absence of physical knowledge in their training data and the lack of embedded physical priors.To tackle the shortfall, we introduce PhysAgent, a novel framework that combines the generalization strengths of VLMs with the specialized expertise of vision models, significantly enhancing VLMs' physical understanding across a variety of tasks, including an 18.4\% improvement on GPT-4o.Furthermore, our results demonstrate that enhancing VLMs' physical world understanding capabilities can help embodied agents such as MOKA.We believe that PhysBench and PhysAgent offer valuable insights and contribute to bridging the gap between VLMs and physical world understanding. Project Page is here