A foundational 1976 short communication presenting a direct, non-iterative method for finding the best rotation matrix between two point sets via eigendecomposition of a cross-covariance matrix.
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 paper 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.
Levinthal’s 1969 perspective paper defined the protein folding paradox by demonstrating the impossibility of random search, establishing the need for kinetic pathways that guide folding faster than thermodynamic equilibration allows.
Weiler et al.’s NeurIPS 2018 paper introducing 3D Steerable CNNs that achieve SE(3) equivariance through group representation theory and spherical harmonic convolution kernels, eliminating the need for rotational data augmentation and improving data efficiency for scientific applications with rotational symmetry like molecular and protein structures.
A comprehensive phylogenomic study dating LUCA to ~4.2 Ga and reconstructing it as a complex, anaerobic acetogen. The authors apply the cross-bracing molecular clock method alongside gene-tree-species-tree reconciliation to infer that LUCA possessed an early immune system and lived within a hydrogen-recycling ecosystem.