Authors: Ertelt, Moritz^1,2 (AUTHOR), Mulligan, Vikram Khipple³ (AUTHOR), Maguire, Jack B.⁴ (AUTHOR), Lyskov, Sergey⁵ (AUTHOR), Moretti, Rocco^6,7 (AUTHOR), Schiffner, Torben¹ (AUTHOR), Meiler, Jens^1,2,6,7 (AUTHOR), Schoeder, Clara T.^1,2 (AUTHOR) clara.schoeder@medizin.uni-leipzig.de

Superior Title: PLoS Computational Biology. 3/14/2024, Vol. 20 Issue 3, p1-20. 20p.

Subject Terms: *POST-translational modification, *PROTEIN engineering, *MACHINE learning, *ENGINEERING design, *COMPUTATIONAL biology, *ARTIFICIAL neural networks, *COMPUTATIONAL neuroscience

Authors: Min, Xiaoping^1,2,3 (AUTHOR), Yang, Chongzhou^1,2 (AUTHOR), Xie, Jun^1,2 (AUTHOR), Huang, Yang^2,4 (AUTHOR), Liu, Nan^2,5 (AUTHOR), Jin, Xiaocheng^2,5 (AUTHOR), Wang, Tianshu^1,2 (AUTHOR), Kong, Zhibo^2,3,5 (AUTHOR), Lu, Xiaoli⁶ (AUTHOR), Ge, Shengxiang^2,3,5 (AUTHOR) sxge@xmu.edu.cn, Zhang, Jun^2,3,5 (AUTHOR), Xia, Ningshao^2,3,5 (AUTHOR)

Superior Title: BMC Bioinformatics. 1/23/2024, Vol. 25 Issue 1, p1-18. 18p.

Subject Terms: *LANGUAGE models, *PROTEIN engineering, *SYNTHETIC proteins, *PROTEIN models, *REINFORCEMENT learning, *AMINO acid sequence

Authors: Zhang, Xing^1,2 (AUTHOR), Yin, Hongmei² (AUTHOR), Ling, Fei¹ (AUTHOR) fling@scut.edu.cn, Zhan, Jian² (AUTHOR), Zhou, Yaoqi² (AUTHOR)

Superior Title: PLoS Computational Biology. 12/7/2023, Vol. 19 Issue 12, p1-25. 25p.

Subject Terms: *PROTEIN engineering, *MULTILAYER perceptrons, *CONVOLUTIONAL neural networks, *DEEP learning, *AMINO acid sequence, *TRANSFORMER models, *SPINE

Authors: Xu, Huanhuan^1,2 (AUTHOR), Yu, Bicheng^1,2 (AUTHOR), Wei, Wanqing² (AUTHOR), Chen, Xiulai² (AUTHOR), Gao, Cong² (AUTHOR), Liu, Jia² (AUTHOR), Guo, Liang² (AUTHOR), Song, Wei^1,2 (AUTHOR), Liu, Liming² (AUTHOR), Wu, Jing¹ (AUTHOR) wujing@jiangnan.edu.cn

Superior Title: Applied Microbiology & Biotechnology. Jun2023, Vol. 107 Issue 11, p3535-3549. 15p.

Subject Terms: *PYRUVATES, *PROTEIN engineering, *ALLOSTERIC regulation, *ENZYME activation, *CANDIDA tropicalis, *CHEMICAL industry

Authors: Höler, Sebastian¹ (AUTHOR), Degreif, Daniel¹ (AUTHOR), Stix, Florentine¹ (AUTHOR), Yang, Shang² (AUTHOR), Gao, Shiqiang² (AUTHOR), Nagel, Georg² (AUTHOR), Moroni, Anna³ (AUTHOR), Thiel, Gerhard^1,4 (AUTHOR), Bertl, Adam^1,4 (AUTHOR), Rauh, Oliver^1,4 (AUTHOR) rauh@bio.tu-darmstadt.de

Superior Title: PLoS ONE. 4/13/2023, Vol. 17 Issue 4, p1-24. 24p.

Subject Terms: *MINING engineering, *PROTEIN engineering, *SACCHAROMYCES cerevisiae, *BLUE light, *CELL growth

Authors: Khatami, Mohammad Hassan¹ (AUTHOR), Mendes, Udson C.² (AUTHOR), Wiebe, Nathan^3,4,5 (AUTHOR), Kim, Philip M.^1,3,6 (AUTHOR) pi@kimlab.org

Superior Title: PLoS Computational Biology. 4/12/2023, Vol. 19 Issue 4, p1-20. 20p. 3 Diagrams, 1 Chart, 4 Graphs.

Subject Terms: *QUANTUM computing, *PROTEIN engineering, *AMINO acid sequence, *QUANTUM computers, *PROTEIN structure, *PROTEIN models

Authors: Hu, Shilong¹ (AUTHOR), Fei, Mingyue¹ (AUTHOR), Fu, Beibei¹ (AUTHOR), Yu, Mingjing¹ (AUTHOR), Yuan, Panhong¹ (AUTHOR), Tang, Biao² (AUTHOR), Yang, Hua² (AUTHOR), Sun, Dongchang¹ (AUTHOR) sundch@zjut.edu.cn

Superior Title: Applied Microbiology & Biotechnology. Apr2023, Vol. 107 Issue 7/8, p2277-2288. 12p.

Subject Terms: *ESCHERICHIA coli, *PROTEIN engineering, *PYRUVATES, *PROBIOTICS, *FERMENTATION, *GENETIC engineering

Authors: Negi, Shigeru¹ (AUTHOR) snegi@dwc.doshisha.ac.jp, Imanishi, Miki² (AUTHOR), Hamori, Mami¹ (AUTHOR), Kawahara-Nakagawa, Yuka³ (AUTHOR), Nomura, Wataru⁴ (AUTHOR), Kishi, Kanae⁴ (AUTHOR), Shibata, Nobuhito¹ (AUTHOR), Sugiura, Yukio¹ (AUTHOR)

Superior Title: Journal of Biological Inorganic Chemistry (JBIC). Apr2023, Vol. 28 Issue 3, p249-261. 13p.

Subject Terms: *ZINC-finger proteins, *PROTEIN engineering, *COMMODITY futures, *AMINO acid residues, *SYNTHETIC proteins, *CYTOSKELETAL proteins

Authors: Hu, Ruyun¹ (AUTHOR) tong.si@siat.ac.cn, Fu, Lihao^1,2,3 (AUTHOR), Chen, Yongcan^1,2 (AUTHOR), Chen, Junyu¹ (AUTHOR), Qiao, Yu¹ (AUTHOR) tong.si@siat.ac.cn, Si, Tong^1,2,3 (AUTHOR) tong.si@siat.ac.cn

Superior Title: Briefings in Bioinformatics. Jan2023, Vol. 24 Issue 1, p1-9. 9p.

Subject Terms: *ROBOTICS, PROTEIN engineering, ENZYME specificity, PROTEIN domains, BIOSURFACTANTS, G proteins, EVOLUTIONARY algorithms

Authors: Garcia-Calvo, Eduardo¹ (AUTHOR) edugar01@ucm.es, García-García, Aina¹ (AUTHOR) ainagarcia@ucm.es, Rodríguez, Santiago¹ (AUTHOR), Martín, Rosario¹ (AUTHOR), García, Teresa¹ (AUTHOR)

Superior Title: Viruses (1999-4915). May2024, Vol. 16 Issue 5, p686. 18p.

Subject Terms: *DNA sequencing, *PROTEIN engineering, *SEQUENCE analysis, *TRANSCRIPTOMES, *LIBRARIES

Authors: Ye, Quanhui¹ (AUTHOR), Wang, Dong² (AUTHOR), Wei, Na¹ (AUTHOR) nawei2@illinois.edu

Superior Title: Trends in Biotechnology. May2024, Vol. 42 Issue 5, p575-590. 16p.

Subject Terms: *RARE earth metals, *PROTEIN engineering, *TECHNOLOGICAL innovations, *BIOMATERIALS, *WASTE recycling, *ENGINEERING

Authors: Ohara, Naoya¹ (AUTHOR), Kawakami, Norifumi¹ (AUTHOR) norikawakami@bio.keio.ac.jp, Arai, Ryoichi^2,3 (AUTHOR), Adachi, Naruhiko^4,5 (AUTHOR), Ikeda, Akihito⁴ (AUTHOR), Senda, Toshiya⁴ (AUTHOR), Miyamoto, Kenji¹ (AUTHOR) kmiyamoto@bio.keio.ac.jp

Superior Title: Chemical Communications. 4/30/2024, Vol. 60 Issue 34, p4605-4608. 4p.

Subject Terms: *PEPTIDES, *PROTEIN engineering, *GREEN fluorescent protein

Authors: Tang, Jiabao^1,2,3,4,5,6 (AUTHOR), Hao, Mengling^1,2,3,4,5,6 (AUTHOR), Liu, Junxian^1,2,3,4,5,6 (AUTHOR), Chen, Yaling^1,2,3,4,5,6 (AUTHOR), Wufuer, Gulimire^1,2,3,4,5,6 (AUTHOR), Zhu, Jie⁷ (AUTHOR), Zhang, Xuejie^1,2,3,4,5,6 (AUTHOR), Zheng, Tingquan^1,2,3,4,5,6 (AUTHOR), Fang, Mujin^1,2,3,4,5,6 (AUTHOR), Zhang, Shiyin^1,2,3,4,5,6 (AUTHOR), Li, Tingdong^1,2,3,4,5,6 (AUTHOR) litingdong@xmu.edu.cn, Ge, Shengxiang^1,2,3,4,5,6 (AUTHOR) sxge@xmu.edu.cn, Zhang, Jun^1,2,3,4,5,6 (AUTHOR), Xia, Ningshao^1,2,3,4,5,6 (AUTHOR)

Superior Title: Communications Chemistry. 4/18/2024, Vol. 7 Issue 1, p1-10. 10p.

Subject Terms: *PROTEIN engineering, *RECOGNITION (Psychology), *CHEMICAL yield, *PEPTIDES, *CATALYTIC activity, *UBIQUITIN ligases, *BIOCONJUGATES

Authors: Stachowski, Timothy R.¹ (AUTHOR), Fischer, Marcus¹ (AUTHOR) marcus.fischer@stjude.org

Superior Title: Journal of Applied Crystallography. Apr2024, Vol. 57 Issue 2, p580-586. 7p.

Subject Terms: *GRAPHICAL user interfaces, *PROTEIN engineering, *PROTEIN models, *BANKING industry, *G protein coupled receptors

Authors: HALLEN, MARK A.^1,2 mhallen@ttic.edu, DONALD, BRUCE R.^2,3,4 brd+cacm19@cs.duke.edu

Superior Title: Communications of the ACM. Oct2019, Vol. 62 Issue 10, p76-84. 9p. 4 Diagrams, 1 Graph.

Subject Terms: *ALGORITHMS, PROTEIN engineering, PAIRED comparisons (Mathematics), PROTEIN stability, CHEMICAL bonds

Authors: Padhi, Aditya K (AUTHOR) aditya.bce@itbhu.ac.in, Tripathi, Timir (AUTHOR) aditya.bce@itbhu.ac.in

Superior Title: Briefings in Functional Genomics. Mar2023, Vol. 22 Issue 2, p195-203. 9p.

Subject Terms: *SARS-CoV-2, *PROTEIN engineering

Authors: Tomoiagă, Raluca Bianca¹ (AUTHOR), Tork, Souad Diana¹ (AUTHOR), Filip, Alina¹ (AUTHOR), Nagy, Levente Csaba¹ (AUTHOR), Bencze, László Csaba¹ (AUTHOR) laszlo.bencze@ubbcluj.ro

Superior Title: Applied Microbiology & Biotechnology. Feb2023, Vol. 107 Issue 4, p1243-1256. 14p.

Subject Terms: *PHENYLALANINE, *PROTEIN engineering, *MUTAGENESIS, *PARSLEY, *STERIC hindrance, *DOPA, *ARABIDOPSIS thaliana, *ELECTRONIC modulators

Authors: Woolley, Michael¹ (AUTHOR), Chen, Zhilei¹ (AUTHOR) zchen4@tamu.edu

Superior Title: PLoS ONE. 10/31/2022, Vol. 17 Issue 10, p1-10. 10p.

Subject Terms: *POLYMERASE chain reaction, *PROTEIN engineering, *AMPLIFICATION reactions, *SYNTHETIC proteins, *GENE libraries, *TRIAZINES, *LIBRARIES, *PROOF of concept

Authors: Foley, Gabriel¹ (AUTHOR), Mora, Ariane¹ (AUTHOR), Ross, Connie M.¹ (AUTHOR), Bottoms, Scott² (AUTHOR), Sützl, Leander³ (AUTHOR), Lamprecht, Marnie L.¹ (AUTHOR), Zaugg, Julian¹ (AUTHOR), Essebier, Alexandra¹ (AUTHOR), Balderson, Brad¹ (AUTHOR), Newell, Rhys¹ (AUTHOR), Thomson, Raine E. S.¹ (AUTHOR), Kobe, Bostjan^1,4 (AUTHOR), Barnard, Ross T.¹ (AUTHOR), Guddat, Luke¹ (AUTHOR), Schenk, Gerhard^1,5 (AUTHOR), Carsten, Jörg⁶ (AUTHOR), Gumulya, Yosephine¹ (AUTHOR), Rost, Burkhard⁷ (AUTHOR), Haltrich, Dietmar³ (AUTHOR), Sieber, Volker^1,2,6 (AUTHOR)

Superior Title: PLoS Computational Biology. 10/24/2022, Vol. 18 Issue 10, p1-35. 35p. 3 Diagrams, 3 Graphs.

Subject Terms: *MAXIMUM likelihood statistics, *PROTEIN engineering, *BIG data, *OXIDOREDUCTASES, *MORPHOLOGY, *MOLECULAR evolution

Authors: Jayaraman, Kumaresan¹ (AUTHOR), Trachtmann, Natalia² (AUTHOR), Sprenger, Georg A.² (AUTHOR) georg.sprenger@imb.uni-stuttgart.de, Gohlke, Holger^1,3 (AUTHOR) gohlke@uni-duesseldorf.de

Superior Title: Applied Microbiology & Biotechnology. Oct2022, Vol. 106 Issue 19/20, p6505-6517. 13p.

Subject Terms: *PROTEIN engineering, *ESCHERICHIA coli, *CORYNEBACTERIUM glutamicum, *BIOACTIVE compounds, *AMINO acids