Journal: bioRxiv

Article Title: What comes after de novo ? Automated lead optimization of proteins with CRADLE-1

doi: 10.64898/2026.03.06.710001

Figure Lengend Snippet: Comparative Pareto frontier analysis for multi-objective scFv optimization. Successive optimization rounds for an anti-Her2 scFv are visualized across three methodologies: cradle-1 (left), an open-source ESM-2-based method (middle), and alanine scan+CDR-DMS with stacking (right). Plots illustrate the trade-off between expression yield ( E. coli ) and thermal stability ( T m ). Successive cradle-1 rounds demonstrate a clear shift toward the high-performance upper-right quadrant.

Article Snippet: Per reaction mix, 5 μL was transformed into either SHuffle® Express Competent E. coli (NEB, C3028) (for anti-SARS VHH and anti-snake venom VHH) or BL21 Competent E. coli (NEB, C2530H) (for haloalkane dehalogenase and serine-pyruvate aminotransferase libraries), following NEB’s instructions.

Techniques: Expressing

Journal: Nature chemical biology

Article Title: Monitoring methionine sulfoxide with stereospecific mechanism-based fluorescent sensors

doi: 10.1038/nchembio.1787

Figure Lengend Snippet: E. coli cells expressing MetSOx ( a ) or MetROx ( b ) were incubated with MetO for ~30 min, and then rinsed to remove the oxidant. Arrows indicate the addition (↓) of MetO and rinsing (↑) the cells for two representative experiments (Assay 1 and Assay 2). MetSOx ( c ) and MetROx ( d ) oxidized fractions calculated from (n = 3), using and , respectively, described in the “ online methods ” section.

Article Snippet: SoluBL21 TM E. coli (Gelantis, San Diego, CA) cells were transformed with an indicated expression vector and grown in Luria-Bertani containing ampicillin (50 μg.ml −1 ) at 37°C.

Techniques: Expressing, Incubation