Joint Protein Sequence and Structure Codesign

SimpleDesign introduces a single-stage end-to-end objective for joint protein sequence and structure codesign, directly modeling in the data space. It combines discrete cross-entropy for sequences and a regression objective for structures using Transformer-based multimodal backbones with modality-specific processing and global self-attention. Trained on over 2M sequence-structure pairs, it achieves competitive performance in co-design and unconditional generation benchmarks.