PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall
Enzymatic digestion of lignocellulosic plant biomass is a key step in bio-refinery approaches for the production of biofuels and other valuable chemicals. However, the recalcitrance of this material in conjunction with its variability and heterogeneity strongly hampers the economic viability and pro...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023003380 |
| _version_ | 1827577642318036992 |
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| author | Partho Sakha De Torben Glass Merle Stein Thomas Spitzlei Adélaïde Raguin |
| author_facet | Partho Sakha De Torben Glass Merle Stein Thomas Spitzlei Adélaïde Raguin |
| author_sort | Partho Sakha De |
| collection | DOAJ |
| description | Enzymatic digestion of lignocellulosic plant biomass is a key step in bio-refinery approaches for the production of biofuels and other valuable chemicals. However, the recalcitrance of this material in conjunction with its variability and heterogeneity strongly hampers the economic viability and profitability of biofuel production. To complement both academic and industrial experimental research in the field, we designed an advanced web application that encapsulates our in-house developed complex biophysical model of enzymatic plant cell wall degradation. PREDIG (https://predig.cs.hhu.de/) is a user-friendly, free, and fully open-source web application that allows the user to perform in silico experiments. Specifically, it uses a Gillespie algorithm to run stochastic simulations of the enzymatic saccharification of a lignocellulose microfibril, at the mesoscale, in three dimensions. Such simulations can for instance be used to test the action of distinct enzyme cocktails on the substrate. Additionally, PREDIG can fit the model parameters to uploaded experimental time-course data, thereby returning values that are intrinsically difficult to measure experimentally. This gives the user the possibility to learn which factors quantitatively explain the recalcitrance to saccharification of their specific biomass material. |
| first_indexed | 2024-03-08T21:30:42Z |
| format | Article |
| id | doaj.art-f59f4e55a2aa41c4919c506c52eb1c1b |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:42Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-f59f4e55a2aa41c4919c506c52eb1c1b2023-12-21T07:32:12ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012154635475PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wallPartho Sakha De0Torben Glass1Merle Stein2Thomas Spitzlei3Adélaïde Raguin4Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany; Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, GermanyInstitute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany; Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, GermanyInstitute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, GermanyInstitute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, GermanyInstitute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany; Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany; Corresponding author at: Institute for Computational Cell Biology, Computer Science department, Heinrich Heine University, Düsseldorf, 40225, Germany.Enzymatic digestion of lignocellulosic plant biomass is a key step in bio-refinery approaches for the production of biofuels and other valuable chemicals. However, the recalcitrance of this material in conjunction with its variability and heterogeneity strongly hampers the economic viability and profitability of biofuel production. To complement both academic and industrial experimental research in the field, we designed an advanced web application that encapsulates our in-house developed complex biophysical model of enzymatic plant cell wall degradation. PREDIG (https://predig.cs.hhu.de/) is a user-friendly, free, and fully open-source web application that allows the user to perform in silico experiments. Specifically, it uses a Gillespie algorithm to run stochastic simulations of the enzymatic saccharification of a lignocellulose microfibril, at the mesoscale, in three dimensions. Such simulations can for instance be used to test the action of distinct enzyme cocktails on the substrate. Additionally, PREDIG can fit the model parameters to uploaded experimental time-course data, thereby returning values that are intrinsically difficult to measure experimentally. This gives the user the possibility to learn which factors quantitatively explain the recalcitrance to saccharification of their specific biomass material.http://www.sciencedirect.com/science/article/pii/S2001037023003380Plant biomassLignocelluloseBio-refineryEnzymatic saccharificationWeb applicationWeb interface |
| spellingShingle | Partho Sakha De Torben Glass Merle Stein Thomas Spitzlei Adélaïde Raguin PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall Computational and Structural Biotechnology Journal Plant biomass Lignocellulose Bio-refinery Enzymatic saccharification Web application Web interface |
| title | PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall |
| title_full | PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall |
| title_fullStr | PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall |
| title_full_unstemmed | PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall |
| title_short | PREDIG: Web application to model and predict the enzymatic saccharification of plant cell wall |
| title_sort | predig web application to model and predict the enzymatic saccharification of plant cell wall |
| topic | Plant biomass Lignocellulose Bio-refinery Enzymatic saccharification Web application Web interface |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023003380 |
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