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For: Capecchi A, Reymond JL. Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning. Biomolecules 2020;10:E1385. [PMID: 32998475 PMCID: PMC7600738 DOI: 10.3390/biom10101385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
1
Orsi M, Reymond JL. Can large language models predict antimicrobial peptide activity and toxicity? RSC Med Chem 2024;15:2030-2036. [PMID: 38911166 PMCID: PMC11187562 DOI: 10.1039/d4md00159a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/19/2024] [Indexed: 06/25/2024]  Open
2
Mei S. A Multi-Label Learning Framework for Predicting Chemical Classes and Biological Activities of Natural Products from Biosynthetic Gene Clusters. J Chem Ecol 2023;49:681-695. [PMID: 37779180 DOI: 10.1007/s10886-023-01452-z] [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: 01/15/2023] [Revised: 08/28/2023] [Accepted: 09/13/2023] [Indexed: 10/03/2023]
3
Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov 2023;22:895-916. [PMID: 37697042 DOI: 10.1038/s41573-023-00774-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 09/13/2023]
4
Akone S, Hug JJ, Kaur A, Garcia R, Müller R. Structure Elucidation and Biosynthesis of Nannosterols A and B, Myxobacterial Sterols from Nannocystis sp. MNa10993. JOURNAL OF NATURAL PRODUCTS 2023;86:915-923. [PMID: 37011180 PMCID: PMC10152446 DOI: 10.1021/acs.jnatprod.2c01143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Indexed: 05/04/2023]
5
Morehouse NJ, Clark TN, McMann EJ, van Santen JA, Haeckl FPJ, Gray CA, Linington RG. Annotation of natural product compound families using molecular networking topology and structural similarity fingerprinting. Nat Commun 2023;14:308. [PMID: 36658161 PMCID: PMC9852437 DOI: 10.1038/s41467-022-35734-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/20/2022] [Indexed: 01/20/2023]  Open
6
de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023;1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [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: 10/17/2023]
7
Ruchawapol C, Fu WW, Xu HX. A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022;104:154324. [PMID: 35841663 PMCID: PMC9259013 DOI: 10.1016/j.phymed.2022.154324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
8
Saldívar-González FI, Medina-Franco JL. Approaches for enhancing the analysis of chemical space for drug discovery. Expert Opin Drug Discov 2022;17:789-798. [PMID: 35640229 DOI: 10.1080/17460441.2022.2084608] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
9
Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022;13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022]  Open
10
Kim HW, Wang M, Leber CA, Nothias LF, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH, Cottrell GW. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. JOURNAL OF NATURAL PRODUCTS 2021;84:2795-2807. [PMID: 34662515 PMCID: PMC8631337 DOI: 10.1021/acs.jnatprod.1c00399] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/04/2023]
11
Capecchi A, Reymond JL. Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning. J Cheminform 2021;13:82. [PMID: 34663470 PMCID: PMC8524952 DOI: 10.1186/s13321-021-00559-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/02/2021] [Indexed: 01/13/2023]  Open
12
Daley SK, Cordell GA. Alkaloids in Contemporary Drug Discovery to Meet Global Disease Needs. Molecules 2021;26:molecules26133800. [PMID: 34206470 PMCID: PMC8270272 DOI: 10.3390/molecules26133800] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 12/15/2022]  Open
13
Medina-Franco JL, Sánchez-Cruz N, López-López E, Díaz-Eufracio BI. Progress on open chemoinformatic tools for expanding and exploring the chemical space. J Comput Aided Mol Des 2021;36:341-354. [PMID: 34143323 PMCID: PMC8211976 DOI: 10.1007/s10822-021-00399-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023]
14
Daley SK, Cordell GA. Natural Products, the Fourth Industrial Revolution, and the Quintuple Helix. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211003029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
15
Peptides in chemical space. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2021.100081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
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