4 min read

Online tools for chemical research

I am tired of searching compounds online. So far, more than 140 Millons substances have been registered for CAS registry number. However, it doesn’t mean CAS has covered all the compounds. In fact, at least three identifiers have been used to let someone find the compounds’ information online.

The first one is CAS registry number. This number is quiet useful to buy standards. However, it’s not free to get access to the full list of CAS registry number. Furthormore, this number is for substance, which is different from compounds. For example, PubChem show the SID and CID for the same compounds. Since substances’ names or numbers have been used for a long time, some mistakes might happen when we could not tell apart different compounds from the same substances.

The second identifier is Simplified Molecular-Input Line-Entry System (SMILES). This identifier could contain the structure information. However, since the standards are not well established, one compound could be linked to multiple SMILES. Such property has been improved by so-called canonical SMILES. However, this identifier still could not be trusted when you want to use them to get other identifier. SMILES is good to generate the molecular structure. However, we all knew 2D structure could not reflact the 3D structure and some software like MOPAC could be used to find the best structure if you want to do some Quantitative structure–activity relationship based prediction.

The third one is from IUPAC. Of course, it’s not IUPAC name because the name has same issue like SMILES. However, IUPAC has trying to generate InChI for compounds with structure information. They also developed InChIKey by hashes on InChI. InChIKey didn’t cover all of the chemical substances and user could generate the InChIKey themselves when they have InChI. So the problem is that if such key could be generated locally, some mistakes or missing of layers in InChI would still give different keys to the same compounds.

Those three indentifers are not perfect. This is the major issue when you use convertor for them such as Chemical Translation Services from UCDavis. You could always find multiple hits from single entry. I know there are lots of indentifers such as PubChem CID and ChemSpider ID. However, they all have own coverages. Some conversions have no U turn.

Anyway this post is not about those issues. I just want to list some databases which might be helpful for researchers doing non-targeted annotation analysis.

Compounds database

  • PubChem is an open chemistry database at the National Institutes of Health (NIH).

  • Chemspider is a free chemical structure database providing fast text and structure search access to over 67 million structures from hundreds of data sources.

  • ChEBI is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

  • CAS numbers

  • eChemPortal provides free public access to information on properties of chemicals. You could find physical chemical Properties, ecotoxicity, environmental fate and behaviour toxicity for certain compounds

Compounds database on certain topic

  • RefMet A Reference list of Metabolite names.

  • CompTox compounds, exposure and toxicity database. Here is related data. This is for environmental study.

  • T3DB is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

  • HMDB is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.

  • Lipid Maps

  • GMDB a multistage tandem mass spectral database using a variety of structurally defined glycans.

  • KEGG is a collection of small molecules, biopolymers, and other chemical substances that are relevant to biological systems.

  • Drugbank is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.

  • FooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology.

  • LMDB is a freely available electronic database containing detailed information about small molecule metabolites found in different livestock species.

  • Zinc is a free database of commercially-available compounds for virtual screening. You could use this database to search commercial information for certain compound’s standards.

  • chemexper is a commercial website for commercially-available compounds.

MS Database with annotation

MS/MS

MS

Online tools

  • Molview to show a 3D structure from 2D structure. The 3D structure source is from PubChem or Corina.

  • mol2chemfig could convert the smiles string into a figure using in LaTeX.

  • molgen generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures.

  • QSPR MD tools list

  • Isotope pattern prediction

  • mfFinder predict formula based on accurate mass

I will appreciate it if you could comment with other useful while available online tools related to non-targeted analysis in this post.