P(all-atom) Is Unlocking New Path For Protein Design

Abstract We introduce Pallatom, an innovative protein generation model capable of producing protein structures with all-atom coordinates. Pallatom directly learns and models the joint distribution P( structure, seq ) by focusing on P( all-atom ), effectively addressing the interdependence between sequence and structure in protein generation. To achieve this, we propose a novel network architecture specifically designed for all-atom protein generation. Our model employs a dual-track framework that tokenizes proteins into residue-level and atomic-level representations, integrating them through a multi-layer decoding process with “traversing” representations and recycling mechanism. We also introduce the atom14 representation method, which unifies the description of unknown side-chain coordinates, ensuring high fidelity between the generated all-atom conformation and its physical structure. Experimental results demonstrate that Pallatom excels in key metrics of protein design, including designability, diversity, and novelty, showing significant improvements across the board. Our model not only enhances the accuracy of protein generation but also exhibits excellent training efficiency, paving the way for future applications in larger and more complex systems.