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
- 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
- Fold your protein!
esmfold GENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN, test
coloresm
orient
ray 1280, 960, async=1
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}
}