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Number Cited by Other Article(s)
1
Wang Y, Han S, Wang Y, Liang Q, Luo W. Artificial Intelligence Technology Assists Enzyme Prediction and Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025;73:7065-7073. [PMID: 40066931 DOI: 10.1021/acs.jafc.4c13201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2025]
2
Yang D, Liang H, Li X, Zhang C, Lu Z, Ma X. Unleashing the potential of microbial biosynthesis of monoterpenes via enzyme and metabolic engineering. Biotechnol Adv 2025;79:108525. [PMID: 39921018 DOI: 10.1016/j.biotechadv.2025.108525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 12/20/2024] [Accepted: 01/27/2025] [Indexed: 02/10/2025]
3
Pimtawong T, Ren J, Lee J, Lee HM, Na D. A review on computational models for predicting protein solubility. J Microbiol 2025;63:e.2408001. [PMID: 39895070 DOI: 10.71150/jm.2408001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 10/29/2024] [Indexed: 02/04/2025]
4
Taguchi H, Niwa T. Reconstituted Cell-free Translation Systems for Exploring Protein Folding and Aggregation. J Mol Biol 2024;436:168726. [PMID: 39074633 DOI: 10.1016/j.jmb.2024.168726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
5
Wei H, Lunin VV, Alahuhta M, Himmel ME, Huang S, Bomble YJ, Zhang M. Streamlining heterologous expression of top carbonic anhydrases in Escherichia coli: bioinformatic and experimental approaches. Microb Cell Fact 2024;23:190. [PMID: 38956607 PMCID: PMC11218372 DOI: 10.1186/s12934-024-02463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]  Open
6
Parthiban S, Vijeesh T, Gayathri T, Shanmugaraj B, Sharma A, Sathishkumar R. Artificial intelligence-driven systems engineering for next-generation plant-derived biopharmaceuticals. FRONTIERS IN PLANT SCIENCE 2023;14:1252166. [PMID: 38034587 PMCID: PMC10684705 DOI: 10.3389/fpls.2023.1252166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
7
Lee HM, Thai TD, Lim W, Ren J, Na D. Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology. J Biotechnol 2023;375:40-48. [PMID: 37652168 DOI: 10.1016/j.jbiotec.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
8
Chen Z, Wang X, Chen X, Huang J, Wang C, Wang J, Wang Z. Accelerating therapeutic protein design with computational approaches toward the clinical stage. Comput Struct Biotechnol J 2023;21:2909-2926. [PMID: 38213894 PMCID: PMC10781723 DOI: 10.1016/j.csbj.2023.04.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 01/13/2024]  Open
9
Patra P, B R D, Kundu P, Das M, Ghosh A. Recent advances in machine learning applications in metabolic engineering. Biotechnol Adv 2023;62:108069. [PMID: 36442697 DOI: 10.1016/j.biotechadv.2022.108069] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
10
Suleman MT, Alkhalifah T, Alturise F, Khan YD. DHU-Pred: accurate prediction of dihydrouridine sites using position and composition variant features on diverse classifiers. PeerJ 2022;10:e14104. [PMID: 36320563 PMCID: PMC9618264 DOI: 10.7717/peerj.14104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/01/2022] [Indexed: 01/21/2023]  Open
11
Pang C, Zhang G, Liu S, Zhou J, Li J, Du G. Engineering sigma factors and chaperones for enhanced heterologous lipoxygenase production in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022;15:105. [PMID: 36217152 PMCID: PMC9552429 DOI: 10.1186/s13068-022-02206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022]
12
Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide. J Microbiol 2022;60:960-967. [DOI: 10.1007/s12275-022-2122-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
13
Tang S, Liao D, Li X, Lin Y, Han S, Zheng S. Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation. ACS Synth Biol 2021;10:2417-2433. [PMID: 34529398 DOI: 10.1021/acssynbio.1c00252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
14
Melo MCR, Maasch JRMA, de la Fuente-Nunez C. Accelerating antibiotic discovery through artificial intelligence. Commun Biol 2021;4:1050. [PMID: 34504303 PMCID: PMC8429579 DOI: 10.1038/s42003-021-02586-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023]  Open
15
Siedhoff NE, Illig AM, Schwaneberg U, Davari MD. PyPEF-An Integrated Framework for Data-Driven Protein Engineering. J Chem Inf Model 2021;61:3463-3476. [PMID: 34260225 DOI: 10.1021/acs.jcim.1c00099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
16
Shukla V, Runthala A, Rajput VS, Chandrasai PD, Tripathi A, Phulara SC. Computational and synthetic biology approaches for the biosynthesis of antiviral and anticancer terpenoids from Bacillus subtilis. Med Chem 2021;18:307-322. [PMID: 34254925 DOI: 10.2174/1573406417666210712211557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/18/2021] [Accepted: 04/25/2021] [Indexed: 11/22/2022]
17
Chen J, Zheng S, Zhao H, Yang Y. Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J Cheminform 2021;13:7. [PMID: 33557952 PMCID: PMC7869490 DOI: 10.1186/s13321-021-00488-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/20/2021] [Indexed: 11/26/2022]  Open
18
Katsimpouras C, Stephanopoulos G. Enzymes in biotechnology: Critical platform technologies for bioprocess development. Curr Opin Biotechnol 2021;69:91-102. [PMID: 33422914 DOI: 10.1016/j.copbio.2020.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/09/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023]
19
Zhou K, Ng W, Cortés-Peña Y, Wang X. Increasing metabolic pathway flux by using machine learning models. Curr Opin Biotechnol 2020;66:179-185. [PMID: 32896771 DOI: 10.1016/j.copbio.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 01/19/2023]
20
Han X, Ning W, Ma X, Wang X, Zhou K. Improving protein solubility and activity by introducing small peptide tags designed with machine learning models. Metab Eng Commun 2020;11:e00138. [PMID: 32642423 PMCID: PMC7334598 DOI: 10.1016/j.mec.2020.e00138] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/26/2020] [Accepted: 06/15/2020] [Indexed: 01/20/2023]  Open
21
Li C, Swofford CA, Sinskey AJ. Modular engineering for microbial production of carotenoids. Metab Eng Commun 2020;10:e00118. [PMID: 31908924 PMCID: PMC6938962 DOI: 10.1016/j.mec.2019.e00118] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/02/2019] [Accepted: 12/08/2019] [Indexed: 12/12/2022]  Open
22
One Pot Use of Combilipases for Full Modification of Oils and Fats: Multifunctional and Heterogeneous Substrates. Catalysts 2020. [DOI: 10.3390/catal10060605] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
23
Kuroda D, Tsumoto K. Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design. J Pharm Sci 2020;109:1631-1651. [DOI: 10.1016/j.xphs.2020.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/25/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022]
24
Mazurenko S, Prokop Z, Damborsky J. Machine Learning in Enzyme Engineering. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04321] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
25
Han X, Zhang L, Zhou K, Wang X. ProGAN: Protein solubility generative adversarial nets for data augmentation in DNN framework. Comput Chem Eng 2019. [DOI: 10.1016/j.compchemeng.2019.106533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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