PIKAChU: a Python-based informatics kit for analysing chemical units

Autor: Barbara R. Terlouw, Sophie P. J. M. Vromans, Marnix H. Medema

Publikováno v: Journal of Cheminformatics, Vol 14, Iss 1, Pp 1-17 (2022)

Abstract As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exi

Externí odkaz: https://doaj.org/article/dbcaeb216882446096e7079775936517

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

Autor: Jeffrey A. van Santen, Grégoire Jacob, Amrit Leen Singh, Victor Aniebok, Marcy J. Balunas, Derek Bunsko, Fausto Carnevale Neto, Laia Castaño-Espriu, Chen Chang, Trevor N. Clark, Jessica L. Cleary Little, David A. Delgadillo, Pieter C. Dorrestein, Katherine R. Duncan, Joseph M. Egan, Melissa M. Galey, F.P. Jake Haeckl, Alex Hua, Alison H. Hughes, Dasha Iskakova, Aswad Khadilkar, Jung-Ho Lee, Sanghoon Lee, Nicole LeGrow, Dennis Y. Liu, Jocelyn M. Macho, Catherine S. McCaughey, Marnix H. Medema, Ram P. Neupane, Timothy J. O’Donnell, Jasmine S. Paula, Laura M. Sanchez, Anam F. Shaikh, Sylvia Soldatou, Barbara R. Terlouw, Tuan Anh Tran, Mercia Valentine, Justin J. J. van der Hooft, Duy A. Vo, Mingxun Wang, Darryl Wilson, Katherine E. Zink, Roger G. Linington

Publikováno v: ACS Central Science, Vol 5, Iss 11, Pp 1824-1833 (2019)

Externí odkaz: https://doaj.org/article/b59bf6e4802544868887630ad09df6bc

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

Autor: Kai Blin, Simon Shaw, Hannah E Augustijn, Zachary L Reitz, Friederike Biermann, Mohammad Alanjary, Artem Fetter, Barbara R Terlouw, William W Metcalf, Eric J N Helfrich, Gilles P van Wezel, Marnix H Medema, Tilmann Weber

Publikováno v: Nucleic Acids Research.

Microorganisms produce small bioactive compounds as part of their secondary or specialised metabolism. Often, such metabolites have antimicrobial, anticancer, antifungal, antiviral or other bio-activities and thus play an important role for applicati

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::b0ad17050262dc94def2e4b98003790d
https://doi.org/10.1093/nar/gkad344

MIBiG 3.0:: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Autor: Barbara R Terlouw, Kai Blin, Jorge C Navarro-Muñoz, Nicole E Avalon, Marc G Chevrette, Susan Egbert, Sanghoon Lee, David Meijer, Michael J J Recchia, Zachary L Reitz, Jeffrey A van Santen, Nelly Selem-Mojica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A A Al-Salihi, Hannah E Augustijn, J Abraham Avelar-Rivas, Luis A Avitia-Domínguez, Francisco Barona-Gómez, Jordan Bernaldo-Agüero, Vincent A Bielinski, Friederike Biermann, Thomas J Booth, Victor J Carrion Bravo, Raquel Castelo-Branco, Fernanda O Chagas, Pablo Cruz-Morales, Chao Du, Katherine R Duncan, Athina Gavriilidou, Damien Gayrard, Karina Gutiérrez-García, Kristina Haslinger, Eric J N Helfrich, Justin J J van der Hooft, Afif P Jati, Edward Kalkreuter, Nikolaos Kalyvas, Kyo Bin Kang, Satria Kautsar, Wonyong Kim, Aditya M Kunjapur, Yong-Xin Li, Geng-Min Lin, Catarina Loureiro, Joris J R Louwen, Nico L L Louwen, George Lund, Jonathan Parra, Benjamin Philmus, Bita Pourmohsenin, Lotte J U Pronk, Adriana Rego, Devasahayam Arokia Balaya Rex, Serina Robinson, L Rodrigo Rosas-Becerra, Eve T Roxborough, Michelle A Schorn, Darren J Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel Udwary, Aruna Vigneshwari, Kristiina Vind, Sophie P J M Vromans, Valentin Waschulin, Sam E Williams, Jaclyn M Winter, Thomas E Witte, Huali Xie, Dong Yang, Jingwei Yu, Mitja Zdouc, Zheng Zhong, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema

Publikováno v: Nucleic Acids Research, 51(D1), D603-D610. Oxford University Press
Terlouw, B R, Blin, K, Navarro-Muñoz, J C, Avalon, N E, Chevrette, M G, Egbert, S, Lee, S, Meijer, D, Recchia, M J J, Reitz, ZL, van Santen, JA, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, S A A, Augustijn, HE, Avelar-Rivas, JA, Avitia-Domínguez, LA, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, V A, Biermann, F, Booth, TJ, Carrion Bravo, VJ, Castelo-Branco, R, Chagas, FO, Cruz-Morales, P, Du, C, Duncan, KR, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, E J N, van der Hooft, J J J, Jati, AP, Kalkreuter, E, Kalyvas, N, Kang, KB, Kautsar, S, Kim, W, Kunjapur, AM, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, J J R, Louwen, N L L, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, L J U, Rego, A, Rex, DAB, Robinson, S, Rosas-Becerra, LR, Roxborough, ET, Schorn, MA, Scobie, DJ, Singh, KS, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, S P J M, Waschulin, V, Williams, SE, Winter, JM, Witte, TE, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, RG, Weber, T & Medema, MH 2023, ' MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters ', Nucleic Acids Research, vol. 51, no. D1, gkac1049, pp. D603-D610 . https://doi.org/10.1093/nar/gkac1049
Terlouw, B R, Blin, K, Navarro-Muñoz, J C, Avalon, N E, Chevrette, M G, Egbert, S, Lee, S, Meijer, D, Recchia, M J J, Reitz, Z L, van Santen, J A, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, S A A, Augustijn, H E, Avelar-Rivas, J A, Avitia-Domínguez, L A, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, V A, Biermann, F, Booth, T J, Carrion Bravo, V J, Castelo-Branco, R, Chagas, F O, Cruz-Morales, P, Du, C, Duncan, K R, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, E J N, van der Hooft, J J J, Jati, A P, Kalkreuter, E, Kalyvas, N, Kang, K B, Kautsar, S, Kim, W, Kunjapur, A M, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, J J R, Louwen, N L L, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, L J U, Rego, A, Rex, D A B, Robinson, S, Rosas-Becerra, L R, Roxborough, E T, Schorn, M A, Scobie, D J, Singh, K S, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, S P J M, Waschulin, V, Williams, S E, Winter, J M, Witte, T E, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, R G, Weber, T & Medema, M H 2023, ' MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters ', Nucleic Acids Research, vol. 51, no. D1, pp. D603–D610 . https://doi.org/10.1093/nar/gkac1049
Terlouw, B R, Blin, K, Navarro-Muñoz, J C, Avalon, N E, Chevrette, M G, Egbert, S, Lee, S, Meijer, D, Recchia, M J J, Reitz, Z L, van Santen, J A, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, S A A, Augustijn, H E, Avelar-Rivas, J A, Avitia-Domínguez, L A, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, V A, Biermann, F, Booth, T J, Carrion Bravo, V J, Castelo-Branco, R, Chagas, F O, Cruz-Morales, P, Du, C, Duncan, K R, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, E J N, van der Hooft, J J J, Jati, A P, Kalkreuter, E, Kalyvas, N, Kang, K B, Kautsar, S, Kim, W, Kunjapur, A M, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, J J R, Louwen, N L L, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, L J U, Rego, A, Rex, D A B, Robinson, S, Rosas-Becerra, L R, Roxborough, E T, Schorn, M A, Scobie, D J, Singh, K S, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, S P J M, Waschulin, V, Williams, S E, Winter, J M, Witte, T E, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, R G, Weber, T & Medema, M H 2023, ' MIBiG 3.0 : a community-driven effort to annotate experimentally validated biosynthetic gene clusters ', Nucleic Acids Research, vol. 51, no. D1, pp. D603–D610 . https://doi.org/10.1093/nar/gkac1049
Nucleic acids research, 51(D1), D603-D610
Nucleic acids research 51 (2023) D1

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5e557bd5c3d2ddd7d6574fc9d08027c2
https://pure.knaw.nl/portal/en/publications/4e99309a-6840-4150-801f-070cfa20d40c

Ecology and genomics of Actinobacteria: new concepts for natural product discovery

Autor: Doris A, van Bergeijk, Barbara R, Terlouw, Marnix H, Medema, Gilles P, van Wezel

Publikováno v: Nature reviews. Microbiology. 18(10)

Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::5fab06e6275d22fb0286594d6c18ba57
https://pubmed.ncbi.nlm.nih.gov/32483324