Mutexa: a computational ecosystem for intelligent protein engineering

ZJ Yang, Q Shao, Y Jiang, C Jurich, X Ran… - Journal of Chemical …, 2023 - ACS Publications
Protein engineering holds immense promise in shaping the future of biomedicine and
biotechnology. This Review focuses on our ongoing development of Mutexa, a …

Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis

Y Jiang, N Ding, Q Shao, SL Stull… - The Journal of …, 2023 - ACS Publications
Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby
influencing catalytic efficiency. However, it remains unknown whether SPD effects originate …

Quantum Mechanical Cluster Models for Calculations on Enzymatic Reaction Mechanisms: Set‐Up and Accuracy

SP de Visser, H Wong, Y Zhang… - … –A European Journal, 2024 - Wiley Online Library
Enzymes turnover substrates into products with amazing efficiency and selectivity and as
such have great potential for use in biotechnology and pharmaceutical applications …

[HTML][HTML] Halide perovskites from first principles: from fundamental optoelectronic properties to the impact of structural and chemical heterogeneity

MR Filip, L Leppert - Electronic Structure, 2024 - pubishingsupport.iopscience.iop.org
Organic-inorganic metal-halide perovskite semiconductors have outstanding and widely
tunable optoelectronic properties suited for a broad variety of applications. First-principles …

Investigating the Non-Electrostatic Component of Substrate Positioning Dynamics

Y Jiang, N Ding, Q Shao, S Stull, Z Cheng, Z Yang - 2023 - chemrxiv.org
Substrate positioning dynamics (SPD) orients the substrate to reactive conformations in the
active site, accelerating enzymatic reactions. However, it remains unknown whether SPD …

SubTuner: a Physics-Guided Computational Tool for Modifying Enzymatic Substrate Preference and Its Application to Anion Methyltransferases

Q Shao, AC Hollenbeak, Y Jiang, BO Bachmann… - 2024 - chemrxiv.org
Engineering enzymes to catalyze non-native substrates is critical for chemical synthesis and
drug development. Although general-purpose computational tools exist, a significant …