3D Molecule Generation is the process of computationally creating three-dimensional molecular structures with valid geometry and chemical properties. It uses methods such as generative models, molecular simulations, and geometric constraints to produce spatial arrangements of atoms that reflect realistic conformations. This approach is used in drug discovery and materials science to design and optimize molecules by enabling control over structure, interactions, and functional properties.
Designing drug molecules is no longer just about generation, but control. NEC Laboratories America introduces MolDiffdAE, a diffusion-based framework that enables precise, multi-objective tuning of 3D molecular properties. By learning a semantic space, researchers can efficiently guide design, accelerating drug discovery and exploration of chemical space.
Controlled generation of 3D molecules is highly valuable in drug design, enabling targeted modifications that preserve core structure and binding-relevant geometry while improving developability-related properties. While equivariant diffusion models achieve state-of-the-art de novo 3D molecule generation, reliably controlling multiple molecular properties remains challenging. A key limitation is structural: diffusion models typically lack an explicit latent space for targeted manipulation. We propose a semantics-guided equivariant autoencoding diffusion model that learns a disentangled semantic embedding of 3D molecules via an auxiliary encoder, to achieve fine-grained control over the generative denoising process. This semantic embedding enables efficient retrieval, random generation and controlled generation. By directly manipulating the embedding, we effectively steer the molecular generation toward desired compositions, shapes and physicochemical properties, and further enhance the generation quality with retrieval-augmented generation (RAG) using the embedding as the query. Importantly, the disentangled embedding offers significant advantages for joint manipulation of multiple properties. Experiments demonstrate precise and data-efficient property control while preserving non-targeted properties.
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NEC Laboratories America, Inc. (NEC Labs) is the US-based center for NEC Corporation’s global network of corporate research laboratories. Our diverse research groups collaborate with industry, academia and governments to provide disruptive solutions to complex problems. A leader in the integration of IT and network technologies with more than 100 years of expertise, NEC provides a combination of products and solutions that cross-utilize the company’s experience and global resources to meet the complex and ever-changing needs of its customers.