ReactPRED: a tool to predict and analyze biochemical reactions

Sivakumar, T.; Giri, Varun; Park, Jin Hwan; Kim, Tae Yong; Bhaduri, Anirban

doi:10.1093/bioinformatics/btw491

Cited by 37 publications

(31 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to scenarios that have made CDK functionality available in larger systems, a number of projects have employed the CDK as a general cheminformatics toolkit. Examples include jCompoundMapper [11], ScaffoldHunter [12, 13], OMG [14], PaDEL [15], ChemDes [16], ReactPRED [17], SMSD [18–20], WhichCyp [21], MetaPrint2D [22], MetFrag [23], and the IUPHAR/BPS Guide to Pharmacology [24], BRENDA [25] and QSAR DataBank [26] databases. A number of such tools were initially developed using older versions of the CDK and are updated to new releases as they are made available.…”

Section: Introductionmentioning

confidence: 99%

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Mayfield²,

et al. 2017

View full text Add to dashboard Cite

Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.Results We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.ConclusionsThis paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.Graphical abstractCDK 2.0 provides new features and improved performance Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-017-0220-4) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Mayfield²,

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Detailed descriptions of both algorithms and their functionalities can be found elsewhere (Delépine et al, 2018;Sivakumar et al, 2016). Both software programmes require a number of inputs to generate biochemical pathways.…”

Section: Automated Generation Of Pathwaysmentioning

confidence: 99%

“…For ReactPRED, the input reaction rules were completely customisable, and the software's reaction rule creation system allows the user to generate tailored reaction rules for specific tasks (Sivakumar et al, 2016). However, this study only utilised ReactPRED's default reaction rule set to generate outputs, i.e., compounds, reactions, and pathways.…”

Section: Comparative Analysis Of Reactpred and Retropath20mentioning

confidence: 99%

“…CC-BY-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted January 3, 2021. ; https://doi.org/10.1101/2020.12.31.425007 doi: bioRxiv preprint 6 reactions (Delépine et al, 2018;Sivakumar et al, 2016). After generating pathways automatically, a pathway curation method was developed for each tool to analyse millions of generated pathways and remove redundant results.…”

mentioning

confidence: 99%

“…In this study, two powerful computational cheminformatics tools, ReactPRED (Sivakumar et al, 2016) and RetroPath2.0 (Delépine et al, 2018) were applied to design novel biochemical pathways to produce three commodity chemicals: benzene, phenol, and 1, 2-propanediol. These target compounds were chosen based on their limited biochemical pathway knowledge (i.e., how many pathways are known in the current biological databases) and global demand.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Designing novel biochemical pathways to commodity chemicals using ReactPRED and RetroPath2.0

Vigrass

Islam

2021

Preprint

View full text Add to dashboard Cite

Commodity chemicals are high-demand chemicals, used by chemical industries to synthesise cocountless chemical products of daily use. For many of these chemicals, the main production process uses petroleum-based feedstocks. Concerns over these limited resources and their associated environmental problems, as well as mounting global pressure to reduce CO2 emissions have motivated efforts to find biochemical pathways capable of producing these chemicals. Advances in metabolic engineering have led to the development of technologies capable of designing novel biochemical pathways to commodity chemicals. Computational software tools, ReactPRED and RetroPath2.0 were utilised to design 49 novel pathways to produce benzene, phenol, and 1,2-propanediol — all industrially important chemicals with limited biochemical knowledge. A pragmatic methodology for pathway curation was developed to analyse thousands and millions of pathways that were generated using the software. This method utilises publicly accessible biological databases, including MetaNetX, PubChem, and MetaCyc to analyse the generated outputs and assign EC numbers to the predicted reactions. The workflow described here for pathway generation and curation can be used to develop novel biochemical pathways to commodity chemicals from numerous starting compounds.

show abstract

Design and engineering of artificial biosynthetic pathways—where do we stand and where do we go?

Sokolova,

Peng,

Haslinger

2023

FEBS Letters

View full text Add to dashboard Cite

The production of commodity and specialty chemicals relies heavily on fossil fuels. The negative impact of this dependency on our environment and climate has spurred a rising demand for more sustainable methods to obtain such chemicals from renewable resources. Herein, biotransformations of these renewable resources facilitated by enzymes or (micro)organisms have gained significant attention, since they can occur under mild conditions and reduce waste. These biotransformations typically leverage natural metabolic processes, which limits the scope and production capacity of such processes. In this mini‐review, we provide an overview of advancements made in the past 5 years to expand the repertoire of biotransformations in engineered microorganisms. This ranges from redesign of existing pathways driven by retrobiosynthesis and computational design to directed evolution of enzymes and de novo pathway design to unlock novel routes for the synthesis of desired chemicals. We highlight notable examples of pathway designs for the production of commodity and specialty chemicals, showcasing the potential of these approaches. Lastly, we provide an outlook on future pathway design approaches.

show abstract

ReactPRED: a tool to predict and analyze biochemical reactions

Abstract: ReactPRED is available at: https://sourceforge.net/projects/reactpred/ CONTACT: anirban.b@samsung.com or ty76.kim@samsung.comSupplementary information: Supplementary data are available at Bioinformatics online.

Cited by 37 publications

References 19 publications

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Designing novel biochemical pathways to commodity chemicals using ReactPRED and RetroPath2.0

Design and engineering of artificial biosynthetic pathways—where do we stand and where do we go?

Contact Info

Product

Resources

About