Field Guide
Docking, screening and simulation
Virtual screening, docking and QM/MM: choosing a method that answers the question you actually have.
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
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…