Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Selenzyme: enzyme selection tool for pathway design

(2018) Pablo Carbonell et al.   BIOINFORMATICS

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

(2018) Baudoin Delépine et al.   METABOLIC ENGINEERING

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

(2017) Noushin Hadadi et al.   Biotechnology Journal

Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol

(2016) Robert Marmulla et al.   BMC BIOCHEMISTRY

Development of a commercial scale process for production of 1,4-butanediol from sugar

(2016) Anthony Burgard et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate–Product Pairs

(2016) Yuki Moriya et al.   Journal of Chemical Information and Modeling

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

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

RxnSim: a tool to compare biochemical reactions: Fig. 1.

(2015) Varun Giri et al.   BIOINFORMATICS

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

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

Profiling the orphan enzymes

(2014) Maria Sorokina et al.   Biology Direct

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

A computational framework for integration of lipidomics data into metabolic pathways

(2014) Noushin Hadadi et al.   METABOLIC ENGINEERING

EC-BLAST: a tool to automatically search and compare enzyme reactions

(2014) Syed Asad Rahman et al.   NATURE METHODS

XTMS: pathway design in an eXTended metabolic space

(2014) Pablo Carbonell et al.   NUCLEIC ACIDS RESEARCH

Finding Sequences for over 270 Orphan Enzymes

(2014) Alexander G. Shearer et al.   PLoS One

ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine

(2012) Yoshihiko Matsuta et al.   BIOINFORMATICS

Assignment of EC Numbers to Enzymatic Reactions with Reaction Difference Fingerprints

(2012) Qian-Nan Hu et al.   PLoS One

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

(2012) Adam Alexander Thil Smith et al.   PLoS Computational Biology

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

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

Genome-wide discovery of missing genes in biological pathways of prokaryotes

(2011) Yong Chen et al.   BMC BIOINFORMATICS

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

(2011) Ottar Rolfsson et al.   BMC Systems Biology

Divergence and Convergence in Enzyme Evolution

(2011) Michael Y. Galperin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Prediction of novel synthetic pathways for the production of desired chemicals

(2010) Ayoun Cho et al.   BMC Systems Biology

DREAMS of metabolism

(2010) Keng Cher Soh et al.   TRENDS IN BIOTECHNOLOGY

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access

(2009) Junfeng Gao et al.   NUCLEIC ACIDS RESEARCH

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

DESHARKY: automatic design of metabolic pathways for optimal cell growth

(2008) Guillermo Rodrigo et al.   BIOINFORMATICS

De novo biosynthetic pathways: rational design of microbial chemical factories

(2008) Kristala L Jones Prather et al.   CURRENT OPINION IN BIOTECHNOLOGY