PLAID is a groundbreaking multimodal generative model that addresses the challenge of simultaneously generating protein sequences and 3D structures by leveraging the latent space of protein folding models. Unlike previous models, PLAID can generate both discrete sequences and continuous all-atom structural coordinates, making it more practical for real-world applications such as drug design. This model can interpret compositional function and organism prompts, and is trained on extensive sequence databases, which are significantly larger than structural databases, allowing for a more comprehensive understanding of protein generation. The PLAID model utilizes a diffusion model over the latent space of protein folding models, specifically using ESMFold, a successor to AlphaFold2. This approach allows for the training of generative models using only sequence data, which is more readily available and less costly than structural data. By learning from this expansive data set, PLAID can decode both sequence and structure from sampled embeddings, effectively using the structural information contained in pretrained protein folding models for protein design tasks. This method is akin to vision-language-action models in robotics, which use vision-language models trained on large-scale data to inform perception and reasoning. To address the challenges of large and complex latent spaces in transformer-based models, PLAID introduces CHEAP (Compressed Hourglass Embedding Adaptations of Proteins), which compresses the joint embedding of protein sequence and structure. This compression is crucial for managing the high-resolution image synthesis-like mapping required for effective protein generation. The approach not only enhances the capability to generate all-atom protein structures but also holds potential for adaptation to other multimodal generation tasks. As the field advances, models like PLAID could be pivotal in tackling more complex systems, such as those involving nucleic acids and molecular ligands, thus broadening the scope of protein design and related applications. Why this matters: PLAID represents a significant step forward in the field of protein generation, offering a more practical and comprehensive approach that could revolutionize drug design and other applications by enabling the generation of useful proteins with specific functions and organism compatibility.
