Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

Reaction Decoder Tool (RDT): extracting features from chemical reactions

(2016) Syed Asad Rahman et al.   BIOINFORMATICS

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

(2016) Hulda S. Haraldsdóttir et al.   PLoS Computational Biology

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database

(2014) Akhil Kumar et al.   Journal of Chemical Information and Modeling

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

(2014) Syed Asad Rahman et al.   NATURE METHODS

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

(2014) Hulda S Haraldsdóttir et al.   Journal of Cheminformatics

Refining carbon flux paths using atomic trace data

(2013) Jon Pey et al.   BIOINFORMATICS

Algorithm for Reaction Classification

(2013) Hans Kraut et al.   Journal of Chemical Information and Modeling

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Automatic reaction mapping and reaction center detection

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

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

Accurate Atom-Mapping Computation for Biochemical Reactions

(2012) Mario Latendresse et al.   Journal of Chemical Information and Modeling

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization

(2011) Eric L. First et al.   Journal of Chemical Information and Modeling

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

(2011) Jan Schellenberger et al.   Nature Protocols

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Open Babel: An open chemical toolbox

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

ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry

(2010) Anthony J Williams et al.   Journal of Cheminformatics