DynamicFlow: Integrating Protein Dynamics into Drug Design
Flow matching model that co-generates ligands and flexible protein pockets, addressing rigid-receptor limitations in …
Computational Biology
InvMSAFold: Fast & Diverse Inverse Folding
A fast, diverse inverse folding method combining deep learning with Potts models to capture full sequence landscapes.
Funnels, Pathways, and Energy Landscapes
Foundational paper establishing the energy landscape theory, folding funnels, and the principle of minimal frustration.
The Drive to Life on Wet and Icy Worlds
A reformulated theory for the origin of life focusing on alkaline hydrothermal vents as electrochemical reactors.
Three Domains of Life: Woese's Phylogenetic Revolution
Woese et al.'s landmark 1990 paper established the three-domain system based on ribosomal RNA phylogeny, revolutionizing …
How to Fold Graciously: The Levinthal Paradox
A perspective paper defining the Grand Challenge of protein folding: distinguishing kinetic pathways from thermodynamic …
The Nature of LUCA and Early Earth System
Phylogenomic reconstruction of LUCA revealing a complex, 4.2 Ga old acetogen living in an established ecosystem.
Generating Mini-Protein Trajectories with GROMACS
Systematic GROMACS workflows for simulating mini-proteins across multiple amino acids to generate diverse MD …
Mini-Protein Trajectory Generation
Automated GROMACS pipeline generating high-fidelity MD trajectories with atomic force extraction for Neural Network …