Lawrence Livermore National Laboratory

Cross-modal protein encoder that aligns ESM-2 sequence embeddings with ProteinMPNN structure embeddings in a shared space for cross-modal retrieval.

Open-source Apache-2.0 reproduction of AlphaFold3 that predicts all-atom structures of proteins, RNA, DNA, small molecules, and their complexes.

Binding free-energy surrogate trained on 1.4M molecular dynamics frames, ranking docking poses ~28,000x faster than physics-based MMGBSA.

Structure-aware adapter that injects chromatin-derived gene regulatory networks into single-cell RNA foundation models like scGPT and scFoundation.