AlphaFold Structure Usage Curation and Limits — Hands-on

Learn how to use AlphaFold structure predictions responsibly inside structural bioinformatics and modeling pipelines. This module explains confidence scores (pLDDT, PAE) , model anatomy, curation and trimming, integration with experimental structures, and practical limits when applying AlphaFold models to docking, MD and design.

AlphaFold Structure Usage Curation and Limits

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Session Index

Session 1 — AlphaFold Predictions, pLDDT & PAE Session 2 — Download, Inspect & Annotate Models Session 3 — Curation, Trimming & Integration Session 4 — Mini Capstone: AF Model QC Dossier

Session 1

Fee: Rs 8800

AlphaFold Predictions, pLDDT & PAE

How AlphaFold style models are generated and what they capture

multiple sequence alignments attention based networks single chain vs complex predictions

Understanding pLDDT and confidence bands

high vs medium vs low confidence regions disorder and flexible segments color schemes and mapping on structure

Predicted aligned error (PAE) and domain relationships

intra domain vs inter domain confidence rigid vs flexible linkers interpreting PAE plots for use cases

Session 2

Fee: Rs 11800

Download, Inspect & Annotate Models

AlphaFold and similar model repositories

AlphaFold DB overview UniProt and cross references search by accession or sequence

Inspecting AlphaFold model files and metadata

PDB and mmCIF predictions per residue pLDDT fields mapping PAE matrices

Annotating domains, motifs and binding regions on AF models

UniProt features and variants active sites and motifs cofactor and ligand pockets

Session 3

Fee: Rs 14800

Curation, Trimming & Integration

Curation and trimming for docking and MD

removing low confidence tails pruning disordered linkers defining construct boundaries

Integrating AF models with experimental structures

superposition with PDB models building chimeras and domain swaps patching missing loops from experiments

Limits, caveats and common misuse patterns

dynamic regions misinterpreted as rigid multimer and interface uncertainties care in using AF for absolute distances

Session 4

Fee: Rs 18800

Mini Capstone: AF Model QC Dossier

Select a target and evaluate AlphaFold predictions

Theory + Practical

Curate, trim and prepare a modeling ready structure

construct definition and chain selection low confidence region handling final coordinate and annotation set

Deliverables: AF usage and limitation report

dossier with pLDDT and PAE summaries curated PDB or mmCIF file clear recommendations for downstream use

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AlphaFold Structure Usage Curation and Limits Training | pLDDT, PAE & Confidence-Aware Modeling

AlphaFold Structure Usage Curation and Limits — Hands-on