Field Guide

Prediction and validation

AlphaFold and its successors, run locally and checked properly: what a prediction is worth and how to tell when a model is wrong.

Other chapters

X-ray and crystallisation Cryo-EM Fundamentals Prediction and validation Protein design AI workflows and chemistry tools Docking, screening and simulation

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mdeller.com 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… mdeller.com ALPHABETTI ↗ a protein sequence logo in 3D, wrapped around its own predicted structure. The amino acid letters themselves, stacked by how strongly a lang… mdeller.com ButtFold ↗ a protein folds in your browser and the trajectory becomes music: contacts forming are note onsets, hydropathy sets pitch, secondary structu… mdeller.com 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… mdeller.com AlphaFraud ↗ Catch AlphaFold where the fold is wrong: weekly, automatically, on freshly deposited human structures mdeller.com ChatPDB ↗ A protein-structure-literate AI assistant for analyzing proteins: RAG for facts, a QLoRA-tuned model for behaviour, and live Biopython/gemmi…

9 articles

14 Oct 2025 · 6 min read 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… 12 Oct 2025 · 6 min read 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… 20 Aug 2025 · 4 min read 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… 7 Dec 2025 · 5 min read 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… 18 Aug 2025 · 2 min read 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… 11 Aug 2025 · 2 min read 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… 1 Sep 2025 · 3 min read 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… 11 Aug 2025 · 1 min read 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… 11 Aug 2025 · 2 min read 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…