novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

Enhancing Retrosynthetic Reaction Prediction with Deep Learning using Multiscale Reaction Classification

(2019) Javier L. Baylon et al.   Journal of Chemical Information and Modeling

Complete biosynthesis of cannabinoids and their unnatural analogues in yeast

(2019) Xiaozhou Luo et al.   NATURE

Molecular Complexity as a Driver for Chemical Process Innovation in the Pharmaceutical Industry

(2019) Seb Caille et al.   JOURNAL OF ORGANIC CHEMISTRY

CF-Targeter: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals

(2019) Shaozhen Ding et al.   ACS Synthetic Biology

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

(2018) Baudoin Delépine et al.   METABOLIC ENGINEERING

Pathway design using de novo steps through uncharted biochemical spaces

(2018) Akhil Kumar et al.   Nature Communications

ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database

(2018) Jie Dong et al.   Journal of Cheminformatics

Planning chemical syntheses with deep neural networks and symbolic AI

(2018) Marwin H. S. Segler et al.   NATURE

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

BRENDA in 2019: a European ELIXIR core data resource

(2018) Lisa Jeske et al.   NUCLEIC ACIDS RESEARCH

Cannabidiol: State of the art and new challenges for therapeutic applications

(2017) Simona Pisanti et al.   PHARMACOLOGY & THERAPEUTICS

Vanillin biosynthetic pathways in plants

(2017) Anish Kundu   PLANTA

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

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

(2016) Pablo Carbonell et al.   NATURAL PRODUCT REPORTS

Updates in Rhea – an expert curated resource of biochemical reactions

(2016) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

(2016) Noushin Hadadi et al.   ACS Synthetic Biology

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

(2015) Noushin Hadadi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Mimicking a natural pathway for de novo biosynthesis: natural vanillin production from accessible carbon sources

(2015) Jun Ni et al.   Scientific Reports

Designing overall stoichiometric conversions and intervening metabolic reactions

(2015) Anupam Chowdhury et al.   Scientific Reports

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

(2014) Masaaki Kotera et al.   BIOINFORMATICS

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities

(2013) Y. Nakamura et al.   PLANT AND CELL PHYSIOLOGY

Automatic reaction mapping and reaction center detection

(2013) William Lingran Chen et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity

(2011) Q.-N. Hu et al.   BIOINFORMATICS

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

eQuilibrator--the biochemical thermodynamics calculator

(2011) A. Flamholz et al.   NUCLEIC ACIDS RESEARCH

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass

(2010) Eric J. Steen et al.   NATURE

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

(2008) Shota Atsumi et al.   NATURE

Engineered biosynthesis of bacterial aromatic polyketides in Escherichia coli

(2008) W. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA