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Protein Structure Prediction for Drug Discovery

3 posts · Nov 2025 – Dec 2025

What this trail covers

AlphaFold continues to be a foundational tool for scientific discovery, enabling researchers to map complex protein structures. This post highlights its application in understanding glycerate kinase (GLYK), a key enzyme in photosynthesis, and engineering more heat-tolerant crops by modifying its structure. The integration of AlphaFold predictions with molecular simulations has proven to be a powerful methodology for achieving insights into enzyme stability under heat stress, leading to the development of a method to map the structure of apoB100, the key protein behind "bad cholesterol" (LDL). This discovery provides a detailed view of the protein's cage-like shell and ribbon-like belt, opening new avenues for precise therapies targeting LDL and the treatment of atherosclerotic cardiovascular disease (ASCVD).

All DeepMind trails
  1. How AlphaFold is helping scientists engineer more heat-tolerant cropsThis post details how researchers used AlphaFold to predict the 3D structure of glycerate kinase (GLYK), an enzyme crucial for photosynthesis. By combining these predictions with molecular simulations, they identified flexible loops in plant GLYK that destabilize at high temperatures. This insight enabled the creation of hybrid enzymes with more rigid loops borrowed from heat-loving algae, resulting in an enzyme stable up to 65°C. This work demonstrates AlphaFold's utility in identifying specific structural weaknesses and guiding protein engineering for improved heat tolerance in crops.
  2. AlphaFold: Five Years of ImpactThis post celebrates the 5-year impact of AlphaFold, highlighting its role in accelerating scientific discovery, enabling new avenues of biological research, and its recognition with a Nobel Prize. It details the widespread adoption of the AlphaFold Protein Database, its use by millions of researchers, and its impact on understanding disease. The post also discusses AlphaFold's transformation of research timelines, cost reduction, and its role in drug discovery through Isomorphic Labs and the development of AlphaFold 3. It mentions the development of related models like AlphaMissense, AlphaGenome, and AlphaProteo, and positions AlphaFold as a template for AI acceleration across all scientific fields.
  3. AlphaFold Reveals a Key Protein Behind Heart DiseaseThis post details how AlphaFold was used in conjunction with cryo-electron microscopy (cryo-EM) to map the structure of the apoB100 protein, the key component of LDL ("bad cholesterol"). The authors describe the process of using AlphaFold to generate atomic-resolution predictions and then refining these predictions against experimental cryo-EM data. This combined approach enabled the detailed visualization of apoB100's structure, which was previously impossible due to its size and complex interactions with fats and other molecules. The breakthrough provides a structural understanding of how LDL becomes harmful, paving the way for more targeted treatments for ASCVD.