GRAPE-WEB: An automated computational redesign web server for improving protein thermostability

Jinyuan Sun; Wenyu Shi; Zhihui Xing; Guomei Fan; Qinglan Sun; Linhuan Wu; Juncai Ma; Yinglu Cui; Bian Wu

doi:10.1002/mlf2.12152

GRAPE-WEB: An automated computational redesign web server for improving protein thermostability

mLife. 2024 Dec 24;3(4):527-531. doi: 10.1002/mlf2.12152. eCollection 2024 Dec.

Authors

Jinyuan Sun^{1

2}, Wenyu Shi³, Zhihui Xing¹, Guomei Fan⁴, Qinglan Sun⁴, Linhuan Wu⁴, Juncai Ma^{4

5}, Yinglu Cui¹, Bian Wu¹

Affiliations

¹ AIM Center, College of Life Sciences and Technology, Beijing University of Chemical Technology, Institute of Microbiology Chinese Academy of Sciences Beijing China.
² University of Chinese Academy of Sciences Beijing China.
³ State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences China Agricultural University Beijing China.
⁴ Microbial Resource and Big Data Center, Institute of Microbiology Chinese Academy of Sciences Beijing China.
⁵ Chinese National Microbiology Data Center (NMDC) Beijing China.

Abstract

We have developed the GReedy Accumulated strategy for Protein Engineering (GRAPE) to improve enzyme stability across various applications, combining advanced computational methods with a unique clustering and greedy accumulation approach to efficiently explore epistatic effects with minimal experimental effort. To make this strategy accessible to nonexperts, we introduced GRAPE-WEB, an automated, user-friendly web server that allows the design, inspection, and combination of stabilizing mutations without requiring extensive bioinformatics knowledge. GRAPE-WEB's robust performance and accessibility provide a comprehensive and adaptable approach to protein thermostability design, suitable for both newcomers and experienced practitioners in the field. The web server is accessible at https://grape.wulab.xyz.