Research graph
References from novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection. Local targets link to admitted publications; unresolved targets remain external evidence.
Metabolic engineering of microbial pathways for advanced biofuels production
10.1016/j.copbio.2011.04.024 · 2011 · External reference
Semisynthetic Artemisinin, the Chemical Path to Industrial Production
10.1021/op4003196 · 2014 · External reference
Biosynthesis, regulation, and engineering of microbially produced branched biofuels
2019 · External reference
Expanding ester biosynthesis in Escherichia coli
10.1038/nchembio.1476 · 2014 · External reference
Advances in biosynthesis of higher alcohols in Escherichia coli
10.1007/s11274-023-03580-w · 2023 · External reference
Lignin valorization: improving lignin processing in the biorefinery
10.1126/science.1246843 · 2014 · External reference
Pathway design using de novo steps through uncharted biochemical spaces
10.1038/s41467-017-02362-x · 2018 · External reference
Exploring the combinatorial space of complete pathways to chemicals
10.1042/bst20170272 · 2018 · External reference
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network
10.1016/j.ymben.2023.06.001 · 2023 · External reference
Enzyme Discovery: Enzyme Selection and Pathway Design
10.1016/bs.mie.2018.04.005 · 2018 · External reference
IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions
10.1016/j.str.2020.08.003 · 2020 · External reference
Promiscuous enzymatic activity-aided multiple-pathway network design for metabolic flux rearrangement in hydroxytyrosol biosynthesis
10.1038/s41467-019-08781-2 · 2019 · External reference
RetroPath2.0: A retrosynthesis workflow for metabolic engineers
10.1016/j.ymben.2017.12.002 · 2018 · External reference
Retropath: automated pipeline for embedded metabolic circuits
10.1021/sb4001273 · 2014 · External reference
A review of computational tools for design and reconstruction of metabolic pathways
10.1016/j.synbio.2017.11.002 · 2017 · External reference
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
10.1093/nar/gkaa230 · 2020 · External reference
RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades
10.1038/s41929-020-00556-z · 2021 · External reference
Biocatalysed synthesis planning using data-driven learning
10.1038/s41467-022-28536-w · 2022 · External reference
RetroGNN: Fast estimation of synthesizability for virtual screening and de novo design by learning from slow retrosynthesis software
2021 · External reference
Reinforcement Learning for Bioretrosynthesis
10.1021/acssynbio.9b00447 · 2020 · External reference
Retro*: Learning Retrosynthetic Planning with Neural Guided A* Search
2020 · External reference
Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy
10.1039/c9sc05704h · 2020 · External reference
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network
10.1016/j.ymben.2023.06.001 · 2023 · External reference
Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites
10.1073/pnas.1818877116 · 2019 · External reference
Selenzyme: enzyme selection tool for pathway design
10.1093/bioinformatics/bty065 · 2018 · External reference
De novo design of luciferases using deep learning
10.1038/s41586-023-05696-3 · 2023 · External reference
Unresolved reference
2021 · External reference
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design
10.1371/journal.pcbi.1009448 · 2021 · External reference
Designing overall stoichiometric conversions and intervening metabolic reactions
10.1038/srep16009 · 2015 · External reference
KEGG: new perspectives on genomes, pathways, diseases and drugs
10.1093/nar/gkw1092 · 2017 · External reference
Updates in Rhea - an expert curated resource of biochemical reactions
10.1093/nar/gkw990 · 2017 · External reference
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
10.1093/nar/gkv1117 · 2016 · External reference
Selenzyme: enzyme selection tool for pathway design
10.1093/bioinformatics/bty065 · 2018 · External reference
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP
10.1038/s41467-022-30970-9 · 2022 · External reference
PathPred: an enzyme-catalyzed metabolic pathway prediction server
10.1093/nar/gkq318 · 2010 · External reference
XTMS: pathway design in an eXTended metabolic space
10.1093/nar/gku362 · 2014 · External reference
enviPath--The environmental contaminant biotransformation pathway resource
10.1093/nar/gkv1229 · 2016 · External reference
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design
10.1371/journal.pcbi.1009448 · 2021 · External reference
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
10.1002/bit.10803 · 2003 · External reference
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
10.1371/journal.pcbi.1000744 · 2010 · External reference
The ribosome binding site calculator
10.1016/b978-0-12-385120-8.00002-4 · 2011 · External reference
EToxPred: A machine learning-based approach to estimate the toxicity of drug candidates
2019 · External reference
Transporter engineering in microbial cell factories: the ins, the outs, and the in-betweens
10.1016/j.copbio.2020.08.002 · 2020 · External reference
AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches
10.1002/prot.25594 · 2018 · External reference
AGGRESCAN3D: Toward the Prediction of the Aggregation Propensities of Protein Structures
10.1007/978-1-4939-7756-7_21 · 2018 · External reference
Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli
10.1128/aem.02046-08 · 2008 · External reference
Machine-learning-guided directed evolution for protein engineering
10.1038/s41592-019-0496-6 · 2019 · External reference
CLADE 2.0: Evolution-Driven Cluster Learning-Assisted Directed Evolution
10.1021/acs.jcim.2c01046 · 2022 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
