PymolFold

Predict your protein in Pymol! Inspired by ColabFold by Sergey O. Visualization inspired by pymol-color-alphafold. Thanks to ESMFold by Meta and the API.

Tested under macOS Monterey Version 12.5.1, Python 3.7.12. Open an issue if ran into any errors.

Usage

  1. Load extension into pymol. In the pymol command prompt:

run https://raw.githubusercontent.com/JinyuanSun/PymolFold/main/predict_structure.py
# try command below in China mainland:
run https://raw.staticdn.net/JinyuanSun/PymolFold/main/predict_structure.py
  1. Fold your protein!

esmfold GENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN, test
coloresm
orient 
ray 1280, 960, async=1

Step 2 Screenshot

Reference

@article{lin2022language,
  title={Language models of protein sequences at the scale of evolution enable accurate structure prediction},
  author={Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and dos Santos Costa, Allan and Fazel-Zarandi, Maryam and Sercu, Tom and Candido, Sal and others},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

GitHub

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