Chemical database

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A chemical database is a

Chemical literature databases correlate structures or other chemical information to relevant references such as academic papers or patents. This type of database includes STN, Scifinder, and Reaxys. Links to literature are also included in many databases that focus on chemical characterization.

Crystallographic database

Most chemical databases store information on stable molecules but in databases for reactions also intermediates and temporarily created unstable molecules are stored. Reaction databases contain information about products, educts, and reaction mechanisms.

Thermophysical database

Thermophysical data are information about

• phase equilibria including vapor–liquid equilibrium, solubility of gases in liquids, liquids in solids (SLE), heats of mixing, vaporization, and fusion
  .
• caloric data like
  heat of formation and combustion
  ,
• transport properties like
  thermal conductivity

• As connection tables / adjacency matrices / lists with additional information on bond (edges) and atom attributes (nodes), such as:

  MDL Molfile, PDB, CML

• As a linear string notation based on
  breadth first traversal
  , such as:

  WLN, InChI

Search by matching 3D conformation of molecules or by specifying spatial constraints is another feature that is particularly of use in drug design. Searches of this kind can be computationally very expensive. Many approximate methods have been proposed, for instance BCUTS, special function representations, moments of inertia, ray-tracing histograms, maximum distance histograms, shape multipoles to name a few.^{[9][10][11][12][13]}

Giga Search

Databases of synthesizable and virtual chemicals are getting larger each year, therefore the ability to efficiently mine them is critical for drug discovery projects. MolSoft's MolCart Giga Search (http://www.molsoft.com/giga-search.html) is the first ever method designed for substructure search of billions of chemicals.

Descriptors

All properties of molecules beyond their structure can be split up into either physico-chemical or

There is no single definition of molecular similarity, however the concept may be defined according to the application and is often described as an

Databases systems for maintaining unique records on chemical compounds are termed as Registration systems. These are often used for chemical indexing, patent systems and industrial databases.

Registration systems usually enforce uniqueness of the chemical represented in the database through the use of unique representations. By applying rules of precedence for the generation of stringified notations, one can obtain unique/'

A key difference between a registration system and a simple chemical database is the ability to accurately represent that which is known, unknown, and partially known. For example, a chemical database might store a molecule with

Registration systems also preprocess molecules to avoid considering trivial differences such as differences in halogen ions in chemicals.

An example is the

List of Chemical Cartridges

• Accord
• Direct ^[16]
• J Chem ^[17]
• CambridgeSoft ^[18]
• Bingo ^[19]
• Pinpoint ^[20]

List of Chemical Registration Systems

• ChemReg ^[21]
• Register^[22]
• RegMol ^[23]
• Compound-Registration ^[24]
• Ensemble ^[25]

Web-based

Tools

The computational representations are usually made transparent to chemists by graphical display of the data. Data entry is also simplified through the use of chemical structure editors. These editors internally convert the graphical data into computational representations.

There are also numerous algorithms for the interconversion of various formats of representation. An open-source utility for conversion is

 SELECT * FROM CHEMTABLE WHERE SMILESCOL.CONTAINS('c1ccccc1')

• Biological database
• Beilstein database and Dortmund Data Bank
• BindingDB
• ChEBI
• ChEMBL
• Chemisches Zentralblatt Structural Database
• ChemSpider
• Collaborative Drug Discovery
• Comparative Toxicogenomics Database
• Computational Chemistry List
• DrugBank
• List of chemical databases
• List of software for molecular mechanics modeling
• LOLI Database
• NMR spectra database
• PubChem
• SPRESI database
• Colocalization Benchmark Source

References