Chemical genomics is an emerging discipline that typically brings together diversity-oriented chemical libraries and high-information-content cellular assays, along with the informatics and mining tools necessary for storing and analysing the data so generated. It is a complement to classical genetics but has at least two advantages: it can be used in genetically non-tractable organisms, and individual chemicals can influence single activities of gene products with multiple roles in a way that gene knockouts and knockins cannot. It is considered especially useful in providing novel tools for the manipulation of cellular activities. Current work is directed to the development and exploitation of these and related methods for the purposes of functional genomics and in mode-of-action studies, concentrating in particular at the level of metabolism. In consequence, we have a particular interest in the relationship between small molecule structures and metabolites, their promiscuous interactions with transporters, their integration into the human metabolic network model, and their eventual use in drug discovery.
As with many things, progress is seen as an iterative cycle between molecular targets and cellular assays, where here we distinguish forward and reverse chemical genetics:
In Forward Chemical Genomics the direction is screen a library to obtain an activity so as to discover a target (this is somewhat like classical drug discovery). In Reverse Chemical Genomics we start with a purified target and assess binding activity whence we can test such compounds in vivo (this is somewhat more akin to modern HTS activities).
Here are some chemical genomics-related links:
- Biochemical pathways (ExPASy) – very useful on-line version of the classic maps
- The Biopathways consortium – developing formalisms for biological pathway analysis
- Brenda – ‘the comprehensive enzyme system’
- COMPANIES – Beyond Genomics – Lipomics – Metabolon – Metabometrix – metanomics – Nutriogenomics – Paradigm Genetics – Phenomenome – Surromed – Target Discovery –
- Ecocyc and metacyc – encyclopedia of E. coli genes and metabolism
- Enzyme nomenclature database at ExPASy.
- GeneCards – for human genes, proteins and diseases
- KEGG – Kyoto encyclopedia of genes and genomes – and the LIGAND enzyme database
- The E-cell project – integrating genomics and metabolism
- Husermet metabolomics LINK scheme
- IUBMB metabolic mini-maps
- Main metabolic pathways on Internet – what it says, plus a nice (and searchable) downloadable version
- Metabolic Control Analysis (MCA), Gepasi, and an on-line review of MCA in the postgenomic era
- Metabolomics.net portal
- Metabolomics papers
- Metabolic pathways portal at NAR
- Metabolomics Society
- Met-Ro project
- MPI for Molecular Plant Physiology – Plant Metabolic profiling
- Minnesota Biocatalysis/Biodegradation Database – pathways primarily for xenobiotic, chemical compounds
- NuGO nutritional metabolomics
- Parasitology metabolomics (Aberystwyth)
- PathBinderH – useful literature tool for metabolomics
- PathDB – a metabolic pathway database which will conceivably link with Gepasi, a metabolic pathway and bio/chemical kinetics simulator written by Pedro Mendes in Aberystwyth; Pedro has now moved to the VBI
- Platform Plant Metabolomics
- Protein Function and Biochemical Pathways (PFBP) at the EBI
- Proteomic Pathway Project (P3)
- The metabolic part of Soybase.
- Reactome – ‘a knowledgebase of biological processes’
- SMRS (Standard metabolite reporting structure)
- WIT – a server linking genes and metabolism, and including metabolic pathways based on the Enzymes and Metabolic Pathways database; See also DBSolve
- Comprehensive Yeast Genome Database, including metabolic pathways. Yeast metabolic network.
CHEMICAL AND DRUG STRUCTURES AND CHEMICAL GENOMICS
- Annotated compound portal at VLS3d – Biocyc and BOCD – BindingDB – BioPharmGuy links – BMRB – CDD – ChEBI – Chembank – ChemDB – ChEMBL – Chembridge – Chemical Universe database – ChemProt – Chemspider – Click2Drug Portal – CML – DART DB – DRAR-CPI – Drugbank – eMolecules dB – EPA toxicology data – HMDB Canada – iPhace – InChI – KEGG – iSpyBio – KeyOrganics – Ligand Depot – MATADOR – Maybridge – METLIN – NCI Cactus Group – NIST species – PDSPKi – PDTD – PharmGKB – PROCOGNATE – PROMISCUOUS – PubChem – PubChem Promiscuity – Purchasable chemicals – SePreSA – Sider2 – SuperTarget – T3DB – TarFisDock – TCDB – TDR Targets – TransPortal – TTD – ZINC –
- Cheminformatics Resources – Cheminformatics links at Fiehn Lab – Cheminformatics links at VLS3d – Chemistry toolkits at VLS3d – Companies portal – Compounds portal – Databases portal – Fragments portal – Indiana Cheminformatics Education Portal – Literature portal – Molecular descriptors (pdf) – QSAR database – UK-QSAR and Cheminformatics group – Software portal – Sung Kwang’s Cheminfo portal – Web services portal – xemistry –
DRUG TRANSPORTER LINKS
For our recent chemical genomics publications – go to the publications page.
Last updated: May 31, 2016 at 9:36 am