Field Guide
Fundamentals
The chemistry already sitting in the Protein Data Bank, and the bonds and switches that the textbooks leave out.
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
Capturing the Invisible: Understanding the Ångström in Structural Biology
Capturing the Invisible: Understanding the Ångström in Structural Biology The ångström equals 1 × 10⁻¹⁰ m, ideal for atomic and molecular dimensions. Named after Anders J…
Elevating Science Communication: Effortless 3D Structure Embedding with 3Dmol.js
Elevating Science Communication: Effortless 3D Structure Embedding with 3Dmol.js Embedding a 3Dmol Viewer 3Dmol.js: molecular visualization with WebGL Instant Deployment:…
Protein Structure and Redox Biology: NOS Linkages as Allosteric Switches
Protein Structure and Redox Biology: NOS Linkages as Allosteric Switches Newly discovered nitrogen-oxygen-sulfur (NOS) linkages in proteins function as dynamic, allosteri…
Hidden Chemistry in the Protein Data Bank: What Else Are We Missing?
Hidden Chemistry in the Protein Data Bank: What Else Are We Missing? Recent research using new machine learning algorithms has uncovered previously undetected nitrogen-ox…