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Number Cited by Other Article(s)
1
Harding-Larsen D, Funk J, Madsen NG, Gharabli H, Acevedo-Rocha CG, Mazurenko S, Welner DH. Protein representations: Encoding biological information for machine learning in biocatalysis. Biotechnol Adv 2024;77:108459. [PMID: 39366493 DOI: 10.1016/j.biotechadv.2024.108459] [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: 04/18/2024] [Revised: 09/19/2024] [Accepted: 09/29/2024] [Indexed: 10/06/2024]
2
Liu L, Liu S, Hu X, Zhou S, Deng Y. Enhancing the activity and succinyl-CoA specificity of 3-ketoacyl-CoA thiolase Tfu_0875 through rational binding pocket engineering. Synth Syst Biotechnol 2024;9:558-568. [PMID: 38694995 PMCID: PMC11061225 DOI: 10.1016/j.synbio.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/04/2024]  Open
3
Harding-Larsen D, Madsen CD, Teze D, Kittilä T, Langhorn MR, Gharabli H, Hobusch M, Otalvaro FM, Kırtel O, Bidart GN, Mazurenko S, Travnik E, Welner DH. GASP: A Pan-Specific Predictor of Family 1 Glycosyltransferase Acceptor Specificity Enabled by a Pipeline for Substrate Feature Generation and Large-Scale Experimental Screening. ACS OMEGA 2024;9:27278-27288. [PMID: 38947828 PMCID: PMC11209901 DOI: 10.1021/acsomega.4c01583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
4
Salvatti BA, Chagas MA, Fernandes PO, Ladeira YFX, Bozzi AS, Valadares VS, Valente AP, de Miranda AS, Rocha WR, Maltarollo VG, Moraes AH. Understanding the Enzyme (S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. J Chem Inf Model 2024;64:4462-4474. [PMID: 38776464 DOI: 10.1021/acs.jcim.3c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
5
Han Y, Zhang H, Zeng Z, Liu Z, Lu D, Liu Z. Descriptor-augmented machine learning for enzyme-chemical interaction predictions. Synth Syst Biotechnol 2024;9:259-268. [PMID: 38450325 PMCID: PMC10915406 DOI: 10.1016/j.synbio.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]  Open
6
Yu Y, Trottmann NF, Schärer MR, Fenner K, Robinson SL. Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater. WATER RESEARCH 2024;256:121593. [PMID: 38631239 DOI: 10.1016/j.watres.2024.121593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
7
Tsutsui Y, Yanaka I, Takeda K, Kondo M, Takizawa S, Kojima R, Konishi A, Yasuda M. Selective recognition between aromatics and aliphatics by cage-shaped borates supported by a machine learning approach. Org Biomol Chem 2024;22:4283-4291. [PMID: 38602393 DOI: 10.1039/d4ob00408f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
8
Wang X, Quinn D, Moody TS, Huang M. ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes. J Chem Inf Model 2024;64:3123-3139. [PMID: 38573056 PMCID: PMC11040732 DOI: 10.1021/acs.jcim.4c00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
9
Ao YF, Dörr M, Menke MJ, Born S, Heuson E, Bornscheuer UT. Data-Driven Protein Engineering for Improving Catalytic Activity and Selectivity. Chembiochem 2024;25:e202300754. [PMID: 38029350 DOI: 10.1002/cbic.202300754] [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: 11/03/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/01/2023]
10
King-Smith E, Faber FA, Reilly U, Sinitskiy AV, Yang Q, Liu B, Hyek D, Lee AA. Predictive Minisci late stage functionalization with transfer learning. Nat Commun 2024;15:426. [PMID: 38225239 PMCID: PMC10789750 DOI: 10.1038/s41467-023-42145-1] [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: 03/27/2023] [Accepted: 10/01/2023] [Indexed: 01/17/2024]  Open
11
Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023;14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [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: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
12
Ge F, Chen G, Qian M, Xu C, Liu J, Cao J, Li X, Hu D, Xu Y, Xin Y, Wang D, Zhou J, Shi H, Tan Z. Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023;71:14911-14930. [PMID: 37800676 DOI: 10.1021/acs.jafc.3c05029] [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: 10/07/2023]
13
Zhang Q, Zheng W, Song Z, Zhang Q, Yang L, Wu J, Lin J, Xu G, Yu H. Machine Learning Enables Prediction of Pyrrolysyl-tRNA Synthetase Substrate Specificity. ACS Synth Biol 2023;12:2403-2417. [PMID: 37486975 DOI: 10.1021/acssynbio.3c00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
14
Clements HD, Flynn AR, Nicholls BT, Grosheva D, Lefave SJ, Merriman MT, Hyster TK, Sigman MS. Using Data Science for Mechanistic Insights and Selectivity Predictions in a Non-Natural Biocatalytic Reaction. J Am Chem Soc 2023;145:17656-17664. [PMID: 37530568 PMCID: PMC10602048 DOI: 10.1021/jacs.3c03639] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
15
Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023;66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
16
Jiang Y, Ran X, Yang ZJ. Data-driven enzyme engineering to identify function-enhancing enzymes. Protein Eng Des Sel 2023;36:gzac009. [PMID: 36214500 PMCID: PMC10365845 DOI: 10.1093/protein/gzac009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/08/2022] [Accepted: 09/28/2022] [Indexed: 01/22/2023]  Open
17
Durairaj J, de Ridder D, van Dijk AD. Beyond sequence: Structure-based machine learning. Comput Struct Biotechnol J 2022;21:630-643. [PMID: 36659927 PMCID: PMC9826903 DOI: 10.1016/j.csbj.2022.12.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]  Open
18
Kovács SC, Szappanos B, Tengölics R, Notebaart RA, Papp B. Underground metabolism as a rich reservoir for pathway engineering. Bioinformatics 2022;38:3070-3077. [PMID: 35441658 PMCID: PMC9154287 DOI: 10.1093/bioinformatics/btac282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]  Open
19
Machine learning modeling of family wide enzyme-substrate specificity screens. PLoS Comput Biol 2022;18:e1009853. [PMID: 35143485 PMCID: PMC8865696 DOI: 10.1371/journal.pcbi.1009853] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/23/2022] [Accepted: 01/21/2022] [Indexed: 11/19/2022]  Open
20
Dudley QM, Cai YM, Kallam K, Debreyne H, Carrasco Lopez JA, Patron NJ. Biofoundry-assisted expression and characterization of plant proteins. Synth Biol (Oxf) 2021;6:ysab029. [PMID: 34693026 PMCID: PMC8529701 DOI: 10.1093/synbio/ysab029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022]  Open
21
Dutta K, Shityakov S, Khalifa I. New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review. Front Bioeng Biotechnol 2021;9:666858. [PMID: 34409018 PMCID: PMC8365754 DOI: 10.3389/fbioe.2021.666858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 01/29/2023]  Open
22
Fenner K, Elsner M, Lueders T, McLachlan MS, Wackett LP, Zimmermann M, Drewes JE. Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence? ACS ES&T WATER 2021;1:1541-1554. [PMID: 34278380 PMCID: PMC8276273 DOI: 10.1021/acsestwater.1c00025] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 05/14/2023]
23
Smith MD, Tassoulas LJ, Biernath TA, Richman JE, Aukema KG, Wackett LP. p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA. Comput Struct Biotechnol J 2021;19:3087-3096. [PMID: 34141132 PMCID: PMC8180931 DOI: 10.1016/j.csbj.2021.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/21/2022]  Open
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