Table 1.
Data sources frequently used for metabolic reconstructions.
| Name | Link | Comment |
|---|---|---|
| Genome Databases | ||
| Comprehensive Microbial Resource (CMR) | http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi. The | |
| Genomes OnLine Database (GOLD) | http://www.genomesonline.org/ | |
| TIGR | http://www.tigr.org/db.shtml | |
| NCBI Entrez Gene | http://www.ncbi.nlm.nih.gov/sites/entrez | |
| SEED database32 | theseed.uchicago.edu/FIG/index.cgi | Comparative genomics tool. |
| Biochemical Databases | ||
| KEGG41 | www.genome.jp/kegg/ | |
| BRENDA42 | www.brenda-enzymes.info/ | |
| Transport DB89 | http://www.membranetransport.org/ | |
| PubChem86 | http://pubchem.ncbi.nlm.nih.gov/ | |
| Transport Classification Database (TCDB) | http://www.tcdb.org/ | TCDB is a curated database of factual information from over 10,000 published references. |
| pKa Plugin | http://www.chemaxon.com/product/pka.html | Free for academic users |
| pKa DB | http://www.acdlabs.com/products/phys_chem_lab/pka/ | Commercial software package to determine acid-base ionization/dissociation constant, pKa. |
| Organism-specific databases | ||
| Ecocyc43 | http://ecocyc.org/ | Escherichia coli database |
| PyloriGene37 | http://genolist.pasteur.fr/PyloriGene | Helicobacter pylori database |
| Gene Cards | www.genecards.org/ | Human gene database |
| Protein Localization databases | ||
| PSORT47 | http://www.psort.org/psortb/ | Support vector machine (SVM) based. |
| PA-SUB48 | http://www.cs.ualberta.ca/~bioinfo/PA/Sub/ | Proteome Analyst Specialized Subcellular Localization Server (SVM based). |
| Bio-numbers | ||
| CyberCell Database (CCDB)88 | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | |
| B10NUMB3R5 | http://bionumbers.hms.harvard.edu/ | |
| Available reconstruction software packages | ||
| Simpheny | http://www.genomatica.com/technology/technologySuite.html | Commercial software |
| COBRA simulation environments | ||
| CellNetAnalyzer90/FluxAnalyzer91 | http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html | Matlab is required |
| COBRA Toolbox16 | http://systemsbiology.ucsd.edu/Downloads/Cobra_Toolbox | Matlab is required |
| FluxExplorer92 | ||
| MetaFluxNet93, 94 | http://mbel.kaist.ac.kr/lab/mfn/ | Stand alone package |