Friends and relatives: insight into conformational regulation from orthologues and evolutionary lineages using KIF and KIN

Dariia Yehorova, Rory M. Crean, Peter M. Kasson and Shina Caroline Lynn Kamerlin

Faraday Discuss., 2024, 252, 341
DOI: 10.1039/D4FD00018H

Interplay Between Substrate Polarity and Protein Dynamics in Evolved Kemp Eliminases

Francesca Peccati, Elizabeth L. Noey, K. N. Houk, Silvia Osuna and Gonzalo Jiménez‐Osés

ChemCatChem, 2024, 16
DOI: 10.1002/cctc.202400444

Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals

Marc Scherer, Sarel J. Fleishman, Patrik R. Jones, Thomas Dandekar and Elena Bencurova

Front. Bioeng. Biotechnol., 2021, 9
DOI: 10.3389/fbioe.2021.673005

A preorganization oriented computational method for de novo design of Kemp elimination enzymes

Shengyu Zhang, Jun Zhang, Wenjia Luo, Pengyu Wang and Yushan Zhu

Enzyme and Microbial Technology, 2022, 160, 110093
DOI: 10.1016/j.enzmictec.2022.110093

Harnessing Conformational Plasticity to Generate Designer Enzymes

Rory M. Crean, Jasmine M. Gardner and Shina C. L. Kamerlin

J. Am. Chem. Soc., 2020, 142, 11324
DOI: 10.1021/jacs.0c04924

Deep learning and generative methods in cheminformatics and chemical biology: navigating small molecule space intelligently

Douglas B. Kell, Soumitra Samanta and Neil Swainston

Biochemical Journal, 2020, 477, 4559
DOI: 10.1042/BCJ20200781

Enhancing catalytic efficiency of Bacillus subtilis laccase BsCotA through active site pocket design

Yiqia Hou, Lijun Zhao, Chen Yue, Jiangke Yang, Yanli Zheng, Wenfang Peng and Lei Lei

Appl Microbiol Biotechnol, 2024, 108
DOI: 10.1007/s00253-024-13291-3

Fishing for Catalysis: Experimental Approaches to Narrowing Search Space in Directed Evolution of Enzymes

Liam R. Marshall, Sagar Bhattacharya and Ivan V. Korendovych

JACS Au, 2023, 3, 2402
DOI: 10.1021/jacsau.3c00315

Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes

Wen Jun Xie and Arieh Warshel

Proc. Natl. Acad. Sci. U.S.A., 2022, 119
DOI: 10.1073/pnas.2207904119

Efficient and easible biocatalysts: Strategies for enzyme improvement. A review

Samah Hashim Albayati, Nima Ghahremani Nezhad, Anmar Ghanim Taki and Raja Noor Zaliha Raja Abd Rahman

International Journal of Biological Macromolecules, 2024, 276, 133978
DOI: 10.1016/j.ijbiomac.2024.133978

Addressing epistasis in the design of protein function

Rosalie Lipsh-Sokolik and Sarel J. Fleishman

Proc. Natl. Acad. Sci. U.S.A., 2024, 121
DOI: 10.1073/pnas.2314999121

Mutexa: A Computational Ecosystem for Intelligent Protein Engineering

Zhongyue J. Yang, Qianzhen Shao, Yaoyukun Jiang, Christopher Jurich, Xinchun Ran, Reecan J. Juarez, Bailu Yan, Sebastian L. Stull, Anvita Gollu and Ning Ding

J. Chem. Theory Comput., 2023, 19, 7459
DOI: 10.1021/acs.jctc.3c00602

In silico design of multipoint mutants for enhanced performance of Thermomyces lanuginosus lipase for efficient biodiesel production

Jinsha Huang, Xiaoman Xie, Wanlin Zheng, Li Xu, Jinyong Yan, Ying Wu, Min Yang and Yunjun Yan

Biotechnol Biofuels, 2024, 17
DOI: 10.1186/s13068-024-02478-5

Modern computational methods for rational enzyme engineering

Pedro Ferreira, Pedro Alexandrino Fernandes and Maria João Ramos

Chem Catalysis, 2022, 2, 2481
DOI: 10.1016/j.checat.2022.09.036

Human GST P1-1 Redesigned for Enhanced Catalytic Activity with the Anticancer Prodrug Telcyta and Improved Thermostability

Aram Ismail, Sridhar Govindarajan and Bengt Mannervik

Cancers, 2024, 16, 762
DOI: 10.3390/cancers16040762

A Rationally Designed c-di-AMP Förster Resonance Energy Transfer Biosensor To Monitor Nucleotide Dynamics

Alex J. Pollock, Philip H. Choi, Shivam A. Zaver, Liang Tong, Joshua J. Woodward and Ann M. Stock

J Bacteriol, 2021, 203
DOI: 10.1128/JB.00080-21

Production of microhomogeneous glycopeptide by a mutated NGT according FuncLib with unique sugar as substrate

Zhaoxi Liu, Kun Li, Xiaoyu Liu, Jiayu Zhao, Yue Yu, Lushan Wang, Yun Kong and Min Chen

Enzyme and Microbial Technology, 2022, 154, 109949
DOI: 10.1016/j.enzmictec.2021.109949

Loop dynamics and the evolution of enzyme activity

Marina Corbella, Gaspar P. Pinto and Shina C. L. Kamerlin

Nat Rev Chem, 2023, 7, 536
DOI: 10.1038/s41570-023-00495-w

Designing better enzymes: Insights from directed evolution

H. Adrian Bunzel, J.L. Ross Anderson and Adrian J. Mulholland

Current Opinion in Structural Biology, 2021, 67, 212
DOI: 10.1016/j.sbi.2020.12.015

Prospects of Using Biocatalysis for the Synthesis and Modification of Polymers

Maksim Nikulin and Vytas Švedas

Molecules, 2021, 26, 2750
DOI: 10.3390/molecules26092750

Current computational methods for enzyme design

Talmage L. Coates, Naomi Young, Austin J. Jarrett, Connor J. Morris, James D. Moody and Dennis Della Corte

Mod. Phys. Lett. B, 2021, 35, 2150155
DOI: 10.1142/S0217984921501554

Repertoire of Computationally Designed Peroxygenases for Enantiodivergent C–H Oxyfunctionalization Reactions

Patricia Gomez de Santos, Ivan Mateljak, Manh Dat Hoang, Sarel J. Fleishman, Frank Hollmann and Miguel Alcalde

J. Am. Chem. Soc., 2023, 145, 3443
DOI: 10.1021/jacs.2c11118

Efficient Base-Catalyzed Kemp Elimination in an Engineered Ancestral Enzyme

Luis I. Gutierrez-Rus, Miguel Alcalde, Valeria A. Risso and Jose M. Sanchez-Ruiz

IJMS, 2022, 23, 8934
DOI: 10.3390/ijms23168934

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

Amol D. Pagar, Mahesh D. Patil, Dillon T. Flood, Tae Hyeon Yoo, Philip E. Dawson and Hyungdon Yun

Chem. Rev., 2021, 121, 6173
DOI: 10.1021/acs.chemrev.0c01201

Cutting-edge computational approaches in enzyme design and activity enhancement

Ruobin Sun, Dan Wu, Pengcheng Chen and Pu Zheng

Biochemical Engineering Journal, 2024, 212, 109510
DOI: 10.1016/j.bej.2024.109510

Preparation, characterization, antimicrobial evaluation, and molecular docking study of paracetamol and niacin mixed-drugs of Mn(II), Fe(II), and Co(II) complexes

Adesoji A. Olanrewaju, Mary A. Adeniyi, Abel K. Oyebamiji, David G. Oke, David O. Adekunle, Sunday A. Akintelu and Omowumi T. Akinola

Discov Appl Sci, 2025, 7
DOI: 10.1007/s42452-025-06548-7

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase

Adriana Coricello, Alanya J. Nardone, Antonio Lupia, Carmen Gratteri, Matthijn Vos, Vincent Chaptal, Stefano Alcaro, Wen Zhu, Yuichiro Takagi and Nigel G. J. Richards

Nat Commun, 2024, 15
DOI: 10.1038/s41467-024-54912-9

Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme–Substrate Complex

Alexander Zlobin and Andrey Golovin

ACS Omega, 2022, 7, 40279
DOI: 10.1021/acsomega.2c05201

Exploiting enzyme evolution for computational protein design

Gaspar P. Pinto, Marina Corbella, Andrey O. Demkiv and Shina Caroline Lynn Kamerlin

Trends in Biochemical Sciences, 2022, 47, 375
DOI: 10.1016/j.tibs.2021.08.008

NMR-guided directed evolution

Sagar Bhattacharya, Eleonora G. Margheritis, Katsuya Takahashi, Alona Kulesha, Areetha D’Souza, Inhye Kim, Jennifer H. Yoon, Jeremy R. H. Tame, Alexander N. Volkov, Olga V. Makhlynets and Ivan V. Korendovych

Nature, 2022, 610, 389
DOI: 10.1038/s41586-022-05278-9

Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design

Alexander Zlobin, Valentina Maslova, Julia Beliaeva, Jens Meiler and Andrey Golovin

J. Chem. Inf. Model., 2025, 65, 2003
DOI: 10.1021/acs.jcim.4c01827

Recent Advances in Biocatalysis for Drug Synthesis

Alina Kinner, Philipp Nerke, Regine Siedentop, Till Steinmetz, Thomas Classen, Katrin Rosenthal, Markus Nett, Jörg Pietruszka and Stephan Lütz

Biomedicines, 2022, 10, 964
DOI: 10.3390/biomedicines10050964

Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase

Eole Fukawa, Yohei Suzuki, Taiki Adachi, Tomoko Miyata, Fumiaki Makino, Hideaki Tanaka, Keiichi Namba, Keisei Sowa, Yuki Kitazumi and Osamu Shirai

Electrochimica Acta, 2024, 490, 144271
DOI: 10.1016/j.electacta.2024.144271