Research graph
References from Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
2010 · External reference
Biosynthesis and secretion of plant cuticular wax
10.1016/s0163-7827(02)00045-0 · 2003 · External reference
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10.1016/j.tplants.2017.01.003 · External reference
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10.1126/science.1217665 · External reference
Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales
10.1111/nph.13441 · 2015 · External reference
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10.1016/s0031-9422(03)00300-5 · External reference
10.1146/annurev.arplant.57.032905.105228
10.1146/annurev.arplant.57.032905.105228 · External reference
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10.1016/j.biopen.2017.12.003 · External reference
10.3390/ijms16023895
10.3390/ijms16023895 · External reference
10.1016/j.copbio.2008.10.011
10.1016/j.copbio.2008.10.011 · External reference
Ecology of Pacific Yew (Taxus brevifolia) in Western Oregon and Washington
10.1046/j.1523-1739.1995.9051189.x-i1 · 1995 · External reference
Engineering salidroside biosynthetic pathway in hairy root cultures of Rhodiola crenulata based on metabolic characterization of tyrosine decarboxylase
10.1371/journal.pone.0075459 · 2013 · External reference
10.1073/pnas.1423555112
10.1073/pnas.1423555112 · External reference
10.1038/s41467-019-09848-w
10.1038/s41467-019-09848-w · External reference
10.1038/nature12051
10.1038/nature12051 · External reference
10.1016/j.biotechadv.2020.107569
10.1016/j.biotechadv.2020.107569 · External reference
10.1038/nchembio.1613
10.1038/nchembio.1613 · External reference
First total synthesis of taxol. 1. Functionalization of the B ring
10.1021/ja00083a066 · 1994 · External reference
Paclitaxel: biosynthesis, production and future prospects
10.1016/j.nbt.2014.02.010 · 2014 · External reference
Flower colour and cytochromes P450
2013 · External reference
10.1126/science.290.5494.1163
10.1126/science.290.5494.1163 · External reference
Molecular and biochemical characterization of 2-hydroxyisoflavanone dehydratase. Involvement of carboxylesterase-like proteins in leguminous isoflavone biosynthesis
10.1104/pp.104.056747 · 2005 · External reference
Managing enzyme promiscuity in plant specialized metabolism: a lesson from flavonoid biosynthesis: Mission of a “body double” protein clarified
10.1002/bies.202000164 · 2021 · External reference
10.1038/nature06450
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10.1016/j.cbpa.2006.08.011
10.1016/j.cbpa.2006.08.011 · External reference
10.1038/nchembio.1476
10.1038/nchembio.1476 · External reference
10.1002/chem.201702235
10.1002/chem.201702235 · External reference
Biocatalysed synthesis planning using data-driven learning
10.1038/s41467-022-28536-w · 2022 · External reference
Unresolved reference
External reference
10.1145/3446776
10.1145/3446776 · External reference
10.1016/j.ymben.2020.10.005
10.1016/j.ymben.2020.10.005 · External reference
10.1093/nar/gkw1092
10.1093/nar/gkw1092 · External reference
10.1093/nar/gkv1070
10.1093/nar/gkv1070 · External reference
10.1093/nar/27.1.29
10.1093/nar/27.1.29 · External reference
10.1093/nar/gkab1028
10.1093/nar/gkab1028 · External reference
10.1093/nar/gki072
10.1093/nar/gki072 · External reference
10.1093/nar/gkx935
10.1093/nar/gkx935 · External reference
MetaCyc: a multiorganism database of metabolic pathways and enzymes
10.1093/nar/gkh100 · 2004 · External reference
EcoCyc: a comprehensive database resource for Escherichia coli
10.1093/nar/gki108 · 2005 · External reference
10.3389/fmicb.2021.711077
10.3389/fmicb.2021.711077 · External reference
10.1093/nar/gkx1012
10.1093/nar/gkx1012 · External reference
Rhea, the reaction knowledgebase in 2022
10.1093/nar/gkab1016 · 2022 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
10.1093/nar/gkab1061
10.1093/nar/gkab1061 · External reference
RetroRules: a database of reaction rules for engineering biology
10.1093/nar/gky940 · 2019 · External reference
10.1093/nar/gkaa971
10.1093/nar/gkaa971 · External reference
10.1093/mp/sst079
10.1093/mp/sst079 · External reference
Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations
10.1021/bi5012833 · 2015 · External reference
The influence of negative training set size on machine learning-based virtual screening
10.1186/1758-2946-6-32 · 2014 · External reference
Handling imbalance classification virtual screening big data using machine learning algorithms
10.1155/2021/6675279 · 2021 · External reference
10.1021/acs.jcim.8b00712
10.1021/acs.jcim.8b00712 · External reference
10.1371/journal.pcbi.1009853
10.1371/journal.pcbi.1009853 · External reference
Tox21challenge to build predictive models of nuclear receptor and stress response pathways as mediated by exposure to environmental chemicals and drugs
2016 · External reference
MolData, a molecular benchmark for disease and target based machine learning
10.1186/s13321-022-00590-y · 2022 · External reference
10.1021/jm0608356
10.1021/jm0608356 · External reference
Efficient feature selection via analysis of relevance and redundancy
2004 · External reference
Unresolved reference
External reference
10.1126/science.181.4096.223
10.1126/science.181.4096.223 · External reference
ProFET: feature engineering captures high-level protein functions
10.1093/bioinformatics/btv345 · 2015 · External reference
10.1021/acs.jcim.0c00073
10.1021/acs.jcim.0c00073 · External reference
Amino acid encoding for deep learning applications
10.1186/s12859-020-03546-x · 2020 · External reference
Learned protein embeddings for machine learning
10.1093/bioinformatics/bty178 · 2018 · External reference
10.1093/nar/gkm998
10.1093/nar/gkm998 · External reference
10.1021/jm9700575
10.1021/jm9700575 · External reference
10.1002/bip.20296
10.1002/bip.20296 · External reference
ChEBI: a database and ontology for chemical entities of biological interest
2008 · External reference
10.1016/j.drudis.2018.02.014
10.1016/j.drudis.2018.02.014 · External reference
10.1016/j.ddtec.2013.01.005
10.1016/j.ddtec.2013.01.005 · External reference
10.1002/minf.201400052
10.1002/minf.201400052 · External reference
10.1111/febs.16274
10.1111/febs.16274 · External reference
Gene ontology annotations and resources
10.1093/nar/gks1050 · 2013 · External reference
InChI version 1.06: now more than 99.99% reliable
10.1186/s13321-021-00517-z · 2021 · External reference
Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics
10.1186/s13321-018-0269-8 · 2018 · External reference
10.1016/j.chempr.2018.02.002
10.1016/j.chempr.2018.02.002 · External reference
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx
10.1038/s41467-022-29238-z · 2022 · External reference
On exploring structure activity relationships
10.1007/978-1-62703-342-8_6 · 2013 · External reference
A guide to machine learning for biologists
10.1038/s41580-021-00407-0 · 2022 · External reference
Unresolved reference
2018 · External reference
10.1186/s13040-017-0155-3
10.1186/s13040-017-0155-3 · External reference
Breaking away from labels: the promise of self-supervised machine learning in intelligent health
10.1016/j.patter.2021.100410 · 2022 · External reference
10.1021/acs.jmedchem.9b02147
10.1021/acs.jmedchem.9b02147 · External reference
10.1093/nar/gkaa1100
10.1093/nar/gkaa1100 · External reference
Modeling aspects of the language of life through transfer-learning protein sequences
10.1186/s12859-019-3220-8 · 2019 · External reference
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
10.1073/pnas.2016239118 · 2021 · External reference
An analysis of protein language model embeddings for fold prediction
10.1093/bib/bbac142 · 2022 · External reference
10.1016/j.str.2022.05.001
10.1016/j.str.2022.05.001 · External reference
10.1038/s41467-021-23303-9
10.1038/s41467-021-23303-9 · External reference
Posttranslational modifications in proteins: resources, tools and prediction methods
2021 · External reference
MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization
10.1093/nar/gkaa275 · 2020 · External reference
Molecular representations in AI-driven drug discovery: a review and practical guide
10.1186/s13321-020-00460-5 · 2020 · External reference
Embedding of molecular structure using molecular hypergraph variational autoencoder with metric learning
10.1002/minf.202000203 · 2021 · External reference
Molecular descriptors for structure-activity applications: a hands-on approach
10.1007/978-1-4939-7899-1_1 · 2018 · External reference
Evaluating self-supervised learning for molecular graph embeddings (arXiv:2206.08005)
2022 · External reference
10.1021/ci00057a005
10.1021/ci00057a005 · External reference
Randomized SMILES strings improve the quality of molecular generative models
10.1186/s13321-019-0393-0 · 2019 · External reference
Unresolved reference
External reference
Yet another representation of molecular structure
10.1021/ci00027a001 · 1995 · External reference
A systematic method for selecting molecular descriptors as features when training models for predicting physiochemical properties
10.1016/j.fuel.2022.123836 · 2022 · External reference
Comparison of descriptor- and fingerprint sets in machine learning models for ADME-Tox targets
10.3389/fchem.2022.852893 · 2022 · External reference
10.1021/ci010132r
10.1021/ci010132r · External reference
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome
10.1186/s13321-020-00445-4 · 2020 · External reference
10.3389/fenvs.2015.00080
10.3389/fenvs.2015.00080 · External reference
Profiling prediction of kinase inhibitors: toward the virtual assay
10.1021/acs.jmedchem.6b01611 · 2017 · External reference
Heterogeneous classifier fusion for ligand-based virtual screening: or, how decision making by committee can be a good thing
10.1021/ci400466r · 2013 · External reference
Kinome-wide profiling prediction of small molecules
10.1002/cmdc.201700180 · 2018 · External reference
10.1021/ci100050t
10.1021/ci100050t · External reference
10.1021/c160017a018
10.1021/c160017a018 · External reference
Using molecular embeddings in QSAR modeling: does it make a difference
10.1093/bib/bbab365 · 2022 · External reference
Retrosynthetic strategies and their impact on synthesis of arcutane natural products
10.1039/d0sc01441a · 2020 · External reference
10.1016/j.coche.2021.100721
10.1016/j.coche.2021.100721 · External reference
10.1039/c9sc03666k
10.1039/c9sc03666k · External reference
10.1002/cjoc.202100273
10.1002/cjoc.202100273 · External reference
Machine learning in computer-aided synthesis planning
2018 · External reference
RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades
10.1038/s41929-020-00556-z · 2021 · External reference
Pathway design using de novo steps through uncharted biochemical spaces
10.1038/s41467-017-02362-x · 2018 · External reference
A deep learning architecture for metabolic pathway prediction
10.1093/bioinformatics/btz954 · 2020 · External reference
ATLAS of biochemistry: a repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies
10.1021/acssynbio.6b00054 · 2016 · External reference
Deep learning in retrosynthesis planning: datasets, models and tools
10.1093/bib/bbab391 · 2022 · External reference
The remarkable pliability and promiscuity of specialized metabolism
10.1101/sqb.2012.77.014787 · 2012 · External reference
10.1021/acs.jcim.8b00801
10.1021/acs.jcim.8b00801 · External reference
10.1007/978-3-030-30493-5_78
10.1007/978-3-030-30493-5_78 · 2019 · External reference
10.1021/acscentsci.7b00303
10.1021/acscentsci.7b00303 · External reference
10.1021/acs.jcim.9b00949
10.1021/acs.jcim.9b00949 · External reference
Unresolved reference
External reference
Learning graph models for retrosynthesis prediction (arXiv:2006.07038)
2021 · External reference
Unresolved reference
External reference
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP
10.1038/s41467-022-30970-9 · 2022 · External reference
10.1093/nar/gkaa992
10.1093/nar/gkaa992 · External reference
Selenzyme: enzyme selection tool for pathway design
10.1093/bioinformatics/bty065 · 2018 · External reference
Identification of enzyme genes using chemical structure alignments of substrate-product pairs
10.1021/acs.jcim.5b00216 · 2016 · External reference
Improved protein-ligand binding affinity prediction with structure-based deep fusion inference
10.1021/acs.jcim.0c01306 · 2021 · External reference
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences
10.1093/bioinformatics/bty535 · 2019 · External reference
The substrate scopes of enzymes: a general prediction model based on machine and deep learning
2022 · External reference
Unresolved reference
2011 · External reference
10.1016/j.coche.2019.08.004
10.1016/j.coche.2019.08.004 · External reference
10.1021/acssynbio.9b00447
10.1021/acssynbio.9b00447 · External reference
10.1038/nature25978
10.1038/nature25978 · External reference
Retro*: Learning Retrosynthetic Planning with Neural Guided A* Search (arXiv:2006.15820)
2020 · External reference
A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis
10.1002/biot.202000605 · 2021 · External reference
10.1021/acs.chemrestox.0c00316
10.1021/acs.chemrestox.0c00316 · External reference
10.3390/ijms19082358
10.3390/ijms19082358 · External reference
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