Field Guide
AI workflows and chemistry tools
Putting language models and chemistry tools into a working structural biology workflow rather than a demo.
Other chapters
X-ray and crystallisation
Cryo-EM
Fundamentals
Prediction and validation
Protein design
AI workflows and chemistry tools
Docking, screening and simulation
Try it
FAFFAbout ↗
forecasts where a protein is likely to stall on the road to a structure, from 335,771 real attempts in the Protein Structure Initiative arch…
ALPHABETTI ↗
a protein sequence logo in 3D, wrapped around its own predicted structure. The amino acid letters themselves, stacked by how strongly a lang…
ButtFold ↗
a protein folds in your browser and the trajectory becomes music: contacts forming are note onsets, hydropathy sets pitch, secondary structu…
TopPDBLX ↗
every crystallisation condition in the protein data bank, parsed and indexed: what worked, how often, and how little of it is specific to yo…
AlphaFraud ↗
Catch AlphaFold where the fold is wrong: weekly, automatically, on freshly deposited human structures
ChatPDB ↗
A protein-structure-literate AI assistant for analyzing proteins: RAG for facts, a QLoRA-tuned model for behaviour, and live Biopython/gemmi…
4 articles
Multi-Step LLM Prompt: From Protein Sequence to Validated Protein Structure
From Sequence to Structure—How LLMs Unlock Protein Mysteries LLMs enable multi-step workflows from raw protein sequence to validated 3D model, combining language and stru…
Supercharging Discovery: How LLM Prompts Are Transforming Structural Biology and Cheminformatics
Supercharging Discovery: How LLM Prompts Are Transforming Structural Biology and Cheminformatics Motif/fingerprint discovery from single protein sequences. Prediction of …
Spacial Score─A Comprehensive Topological Indicator for Small-Molecule Complexity
Spacial Score: A Comprehensive Topological Indicator for Small-Molecule Complexity Spacial Score─A Comprehensive Topological Indicator for Small-Molecule Complexity Optim…
Remapping the Chemical and Pharmacological Spaces of Drugs: Navigating Tomorrow’s Therapeutic Frontier
Remapping the Chemical and Pharmacological Spaces of Drugs: Navigating Tomorrow’s Therapeutic Frontier Remapping the Chemical Space and the Pharmacological Space of Drugs…