Field Guide
How structures get made.
How structures actually get made: crystallisation, cryo-EM, prediction and design, grouped into chapters that each link to a tool you can run.
7 chapters, 48 articles
X-ray and crystallisation
9
Cryo-EM
6
Fundamentals
4
Prediction and validation
9
Protein design
12
AI workflows and chemistry tools
4
Docking, screening and simulation
4
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…
1. X-ray and crystallisation
9 articlesGetting a crystal and getting data from it: screens, harvesting, mounting, microfluidics and what protein stability has to do with any of it.
Unlocking Membrane Protein Structures: The Crystallization Revolution Reshaping Drug Discovery
Unlocking Membrane Protein Structures: The Crystallization Revolution Reshaping Drug Discovery GPCRdb G protein-coupled receptors (GPCRs): advances in structures, mechani…
Revolutionizing Protein Crystallography: The Synergy of TELSAM-DARPin Fusion and Electric Field Optimization
Revolutionizing Protein Crystallography: The Synergy of TELSAM-DARPin Fusion and Electric Field Optimization Engineering Protein Linkers for Optimized TELSAM-DARPin Fusio…
Engineering Protein Stability: Unlocking the Secrets of Successful Crystallization
Engineering Protein Stability: Unlocking the Secrets of Successful Crystallization Modern construct design leverages computational tools like AlphaFold3 and specialized s…
AXIS: Closing the Loop on Crystal Detection
AXIS: Closing the Loop on Crystal Detection AXIS: a Lab-in-the-Loop machine learning approach for automated detection of macromolecular crystals Persistent bottleneck res…
2014 – Approaches to automated protein crystal harvesting
Approaches to automated protein crystal harvesting Link to Paper Precision Robotics: Six-axis anthropomorphic robots achieve submicron positioning accuracy for crystals a…
2015 – Protein stability: a crystallographer’s perspective
Protein stability: a crystallographer’s perspective Link to Paper Protein stability is a critical factor for producing homogeneous, well-ordered crystals, which are essen…
Universal Mounting Robot (UMR)
Universal Mounting Robot (UMR) ACA Poster 2013 Approaches to automated protein crystal harvesting Link Persistent bottleneck in structural biology: crystal harvesting rem…
Top96 Crystal Screen
Top96 Crystal Screen Design Top 96 Conditions Top 96 Poster Commercially available from Rigaku Reagents Large-scale analysis: millions of crystallization trials revealed …
Tiny Pipes, Big Discoveries: How Microfluidics Are Accelerating Structural Biology
Tiny Pipes, Big Discoveries: How Microfluidics Are Accelerating Structural Biology Microfluidics and “lab-on-a-chip” technology are automating and miniaturizing complex l…
2. Cryo-EM
6 articlesSingle particles, tomography and membrane proteins: where cryo-EM now beats crystallography and where it still does not.
Outrunning Diffusion: The Fast Lane in CryoEM Grid Preparation
Outrunning Diffusion: The Fast Lane in CryoEM Grid Preparation Outrunning protein diffusion to the air–water interface in cryoEM Hyperquenching: Nanosecond vitrification …
Revolutionary Cryo-EM Breakthrough: Di-Gembodies Transform Small Protein Structure Determination
Revolutionary Cryo-EM Breakthrough: Di-Gembodies Transform Small Protein Structure Determination Di-Gembodies Size Barrier Elimination: Di-Gembodies enable cryo-EM struct…
Revolutionizing Protein Structure Determination: How MICA Combines Cryo-EM and AlphaFold3 for Unprecedented Accuracy
Revolutionizing Protein Structure Determination: How MICA Combines Cryo-EM and AlphaFold3 for Unprecedented Accuracy Revolutionary Integration: MICA combines cryo-EM expe…
Revolutionizing Protein Structure Analysis: Cryo-EM without Purification Accelerates the Future of Structural Biology
Revolutionizing Protein Structure Analysis: Cryo-EM without Purification Accelerates the Future of Structural Biology New workflow enables solving protein structures via …
Cryo-EM and the New Frontier in Membrane Protein Drug Design
Cryo-EM and the New Frontier in Membrane Protein Drug Design Cryo-EM advancements now enable the high-resolution structural determination of challenging membrane proteins…
Beyond the Microscope: How Cryo-ET is Revealing Disease in Its Native State
Beyond the Microscope: How Cryo-ET is Revealing Disease in Its Native State Cryo-electron tomography (Cryo-ET) allows scientists to visualize protein structures within th…
3. Fundamentals
4 articlesThe chemistry already sitting in the Protein Data Bank, and the bonds and switches that the textbooks leave out.
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…
4. Prediction and validation
9 articlesAlphaFold and its successors, run locally and checked properly: what a prediction is worth and how to tell when a model is wrong.
Revolutionary Bridge Between Prediction and Reality: How Elastic Networks Transform AlphaFold2’s Structural Accuracy
Revolutionary Bridge Between Prediction and Reality: How Elastic Networks Transform AlphaFold2’s Structural Accuracy Flexible fitting of AlphaFold2-predicted models to cr…
The Memorization Trap: Have Protein-Ligand Cofolding Methods Transcended Simple Data Recall?
The Memorization Trap: Have Protein-Ligand Cofolding Methods Transcended Simple Data Recall? Have protein-ligand cofolding methods moved beyond memorisation? Memorization…
Engineering the Future of Proteins: Unveiling the Latest AI Tools Transforming Structural Biology in 2025
Engineering the Future of Proteins: Unveiling the Latest AI Tools Transforming Structural Biology in 2025 AlphaFold 3 refines bound-state predictions for drug discovery b…
Transforming Antibody Design: How Artificial Intelligence Revolutionizes Structure Prediction
Transforming Antibody Design: How Artificial Intelligence Revolutionizes Structure Prediction Review of Antibody Structure Prediction-Based on Artificial Intelligence Rap…
Alphafold Local Install on Mac
Alphafold Local Install on Mac Why Install AlphaFold Locally? Full Control & Independence: Run protein structure predictions without relying on cloud services, API limits…
How AI Is Revealing the Secret Pathways of Protein Folding
How AI Is Revealing the Secret Pathways of Protein Folding Building on structure prediction tools like AlphaFold, AI is now being used to map the entire folding pathway o…
2015 – Models of protein–ligand crystal structures: trust, but verify
Models of protein–ligand crystal structures: trust, but verify Click to enlarge Link to Paper Model Fidelity: Evaluate ligand fit using cLDDT and pocket RMSD before analy…
2013 – Models of protein–ligand crystal structures: trust, but verify
Models of protein–ligand crystal structures: trust, but verify Click to enlarge X-ray crystallography provides precise, high-resolution 3D protein-ligand structures criti…
2017 – Validation of Protein–Ligand Crystal Structure Models: Small Molecule and Peptide Ligands
Validation of Protein–Ligand Crystal Structure Models: Small Molecule and Peptide Ligands Link to Paper Map Fit: Ensure each ligand atom is supported by clear electron de…
5. Protein design
12 articlesGenerative and modular design, from backbone diffusion to the modelling you can run on a laptop.
Protein Hunter: Pioneering the Next Frontier of AI-Driven Protein Design
Protein Hunter: Pioneering the Next Frontier of AI-Driven Protein Design Protein Hunter: exploiting structure hallucination within diffusion for protein design Revolution…
Revolutionizing Drug Discovery: LatentX and the Future of Protein Binder Design
Revolutionizing Drug Discovery: LatentX and the Future of Protein Binder Design LatentX generates lab-functional protein binders with picomolar affinities and near-perfec…
The New Architects: How Generative AI Is Designing Novel Protein Scaffolds
The New Architects: How Generative AI Is Designing Novel Protein Scaffolds The past, present and future of de novo protein design. Nature, 2026 From renovation to archite…
Building Proteins Brick by Brick: How AI Is Assembling Novel Bio-Machines
Building Proteins Brick by Brick: How AI Is Assembling Novel Bio-Machines AI models like ProDomino are being developed to predict how to successfully combine different pr…
AI-Driven Inverse Protein Folding: Transforming Protein Design for Next-Gen Therapeutics
AI-Driven Inverse Protein Folding: Transforming Protein Design for Next-Gen Therapeutics Advanced AI models are solving the “inverse folding problem,” allowing scientists…
The Protein Architect: How Generative AI Is Building the Drugs of Tomorrow
The Protein Architect: How Generative AI Is Building the Drugs of Tomorrow Generative AI has evolved from predicting existing protein structures to designing entirely new…
Beyond Trial and Error: AI-Driven Design of Peptide Therapeutics
Beyond Trial and Error: AI-Driven Design of Peptide Therapeutics AI is transforming peptide drug discovery by replacing slow, trial-and-error methods with rapid, in silic…
What If Protein Structures Could Be Designed Like LEGO? Modular Approaches in 2025
What If Protein Structures Could Be Designed Like LEGO? New AI models are enabling a modular, “LEGO-like” approach to protein design, where proteins are assembled from de…
Compositional Protein Design: Building Proteins from 3D Ellipsoid Blueprints
Compositional Protein Design: Building Proteins from 3D Ellipsoid Blueprints ProtComposer is a new AI model that generates protein structures based on a user-defined layo…
Flow-Based Models: A New Paradigm for Protein Structure Generation
Flow-Based Models: A New Paradigm for Protein Structure Generation Flow-based generative models like Proteina are an emerging alternative to diffusion models for designin…
Generative AI for Protein Pocket Design: The Next Leap in Drug Discovery
Generative AI for Protein Pocket Design: The Next Leap in Drug Discovery New generative AI models like PocketGen can design novel protein binding pockets from scratch, ta…
Installation of RFdiffusion on MacOSX M1 architecture without GPU support
Installation of RFdiffusion on MacOSX M1 architecture without GPU support Rosetta/DGL Issues: Some advanced functionalities (like DGL-based graph operations) may still fa…
6. AI workflows and chemistry tools
4 articlesPutting language models and chemistry tools into a working structural biology workflow rather than a demo.
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…
7. Docking, screening and simulation
4 articlesVirtual screening, docking and QM/MM: choosing a method that answers the question you actually have.
Unleashing Dynamic Precision: How DRGSCROLL Transforms Protein–Ligand Docking
Unleashing Dynamic Precision: How DRGSCROLL Transforms Protein–Ligand Docking Evolutionary side-chain optimization reveals true binding interactions. Automated rotamer se…
Optimizing Data Volume and Diversity for Robust Antibody–Antigen ΔΔG Prediction
Optimizing Data Volume and Diversity for Robust Antibody–Antigen ΔΔG Prediction Volume Expansion: Hundreds of experimental ΔΔG measurements must scale to hundreds of thou…
Revolutionizing Drug Discovery: The Click2Drug Platform and the Rise of AI-Powered Virtual Screening
Revolutionizing Drug Discovery: The Click2Drug Platform and the Rise of AI-Powered Virtual Screening Comprehensive Resource Integration: Click2Drug bridges computational …
The Quantum Leap in Drug Design: Using QM/MM to Predict Perfect Fits
The Quantum Leap in Drug Design: Using QM/MM to Predict Perfect Fits Hybrid QM/MM methods combine quantum mechanics and classical mechanics to model drug-protein interact…