Interesting Cheminformatics Sites and Services Using the JME Editor

Molecular Databases and Chemical Search Engines

ZINC a free database of commercially-available compounds for virtual screening.
Kinase SARfari an integrated chemogenomics workbench focussed on Kinases. It incorporated and links Kinase sequence, structure, compounds and screening data.
Chemical Structure Lookup Service search over 46 million unique structures.
PDBeChem dictionary of chemical components (ligands and small molecules) referred in PDB entries.
ChemBank a public, web-based informatics environment containing data derived from small molecules and small-molecule screens.
QueryChem combine text and chemical structure web searches.
ChemSynthesis freely accessible database of more than 40,000 compounds and more than 45,000 synthesis references.
Mobyle@RPBS a portal for bioinformatics analyses.
JHetChem search for structures in the Journal of Heterocyclic Chemistry.
ChemExper the goal of this project is to create a common and freely accessible database of chemicals over the internet.
Sigma-Aldrich a catalogue of commercial compound provider.
TCI America a catalogue of commercial compound provider.

Databases of Metabolites and Metabolic Reactions

BRENDA the main collection of enzyme functional data available to the scientific community.
3DMET a 3-dimensional structure database of natural metabolites.
BioMeta a database of metabolites and metabolic reactions
MetaCyc a database of nonredundant, experimentally elucidated metabolic pathways containing more than 1,400 pathways from more than 1,800 different organisms.
METLIN microbes metabolite search.

Calculation of Molecular Properties and Molecular Descriptors, Property Lookup

Virtual Computational Chemistry Laboratory calculation of logP and solubility.
Molinspiration Properties logP, TPSA, Rule of 5 descriptors.
Landolt-Boernstein Substance Search in 160,000 substances and their properties which are reported on in the indexed Landolt-Boernstein volumes.
NMR Spectra Lookup InChIKey-based lookup of experimental NMR spectra.

Prediction of Biological Activity and Toxicity

Molinspiration Bioactivity Prediction prediction of activity as GPCR ligands, kinase inhibitors, ion channel blockers and nuclear receptor ligands.
EPA DSSTox distributed structure-searchable toxicity database network.
MetaPrint2D metabolic site predictor.

Generation of 3D Molecular Structures

GALAXY download of 3D structures as Molfiles, display of hydrophobicity potential.
CORINA online demo of 3D structure generator.
ICM online demo of 2D to 3D coverter.
Dundee PRODRG2 Server download of generatred structures in several formats.

Miscellaneous Cheminformatics Services

OSRA chemical optical structure recognition.
AsteriX automated Structure Extraction from PDFs
ChemDB / Virtual Chemical Space retro-synthesis and combinatorial library design
Online SMILES translator SMILES translator and structure file generator.
3D-Mind maps of screening data which lend themselves biochemical understanding and hypothesis generation.

Chemical Education

Virtual Textbook of Organic Chemistry  
O=CHem an introduction to organic chemistry.
Chem 150 survey of biochemistry.

If you have any suggestions or comments concerning this list, or if you want to report a broken link, mail please to peter[dot]ertl[at]gmail[dot]com.

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Updated: May 2011