This paper introduces DynamicFlow, a full-atom stochastic flow matching model that simultaneously generates ligand molecules and transforms protein pockets from apo to holo states. It also contributes a new dataset of MD-simulated apo-holo pairs derived from MISATO.
InvMSAFold replaces autoregressive decoding with a Potts model parameter generator, enabling diverse protein sequence sampling orders of magnitude faster than ESM-IF1.
This seminal work resolves Levinthal’s paradox by replacing the single-pathway view with a statistical energy landscape approach. It introduces the concepts of the folding funnel, the glass transition in proteins, and the ‘stability gap’ as a design principle for foldable sequences.
This paper reformulates the submarine alkaline hydrothermal theory for the origin of life, positing that life emerged as a free energy converter driven by specific geological disequilibria - specifically redox and pH gradients across inorganic precipitate membranes - utilizing hydrogen, methane, and CO2 as primary feedstocks.
A comprehensive phylogenomic study dating LUCA to ~4.2 Ga and reconstructing it as a complex, anaerobic acetogen. The authors employ a novel cross-bracing molecular clock method and gene-tree-species-tree reconciliation to infer that LUCA possessed an early immune system and lived within a hydrogen-recycling ecosystem.