Predicted Protein Structure: GFP, Folded and Scored
Video · 0:47 · Published Invalid Date · Talindrew team
About this video
Green fluorescent protein from a line of amino acids to its predicted beta barrel: search predicted structures by name or UniProt accession in the Model Hub, view the structure coloured by pLDDT confidence with the less certain termini picked out, save it into a notebook entry beside the plasmid that encodes it, and follow the FoldRx pipeline from sequence to ranking.
Structure: AlphaFold DB model AF-P42212-F1 (EMBL-EBI), CC BY 4.0.
What you will learn
- How to find a predicted structure by name or UniProt accession.
- What pLDDT confidence colours mean on a predicted structure.
- Which stages the FoldRx drug discovery pipeline runs, in order.
Transcript
- 0:00
Sequence
Every protein starts as a line of amino acids.
- 0:05
Structure search
Search predicted structures by name or accession, right inside the Model Hub.
- 0:11
The fold
Pick one, and its predicted structure folds up in three dimensions.
- 0:17
pLDDT confidence
Colour it by confidence: deep blue where the model is sure, orange where it is guessing.
- 0:25
Save to notebook
Save the fold into your notebook, next to the plasmid that encodes it.
- 0:30
FoldRx
And for drug discovery, FoldRx chains folding, pocket detection, docking and ADMET into one pipeline. Talindrew. From sequence to structure, in one tab.
Try it on your own sequences.
Free to use. No download required. Works in any modern browser.