Editing Chemical database (section)

==Types of chemical databases ==

=== Bioactivity database ===

Bioactivity databases correlate structures or other chemical information to bioactivity results taken from [[bioassays]] in literature, patents, and screening programs.

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{| class="wikitable sortable"
|-
! Name
! Developer(s)
! Initial release
|-
| [[ScrubChem]]
| [[Jason Bret Harris]]
| 2016<ref>{{Cite web |title=Home Page - ScrubChem |url=http://www.scrubchem.org |archive-url=https://web.archive.org/web/20170526174142/http://www.scrubchem.org/ |archive-date=26 May 2017 |website=scrubchem.org}}</ref><ref>{{cite book| pmid=30848455 | doi=10.1007/978-1-4939-9089-4_3 | volume=1939 | chapter=Post-processing of Large Bioactivity Data | year=2019 | series=Methods Mol Biol | pages=37–47 | last1 = Harris | first1 = JB| title=Bioinformatics and Drug Discovery | isbn=978-1-4939-9088-7 | s2cid=73493315 }}</ref>
|-
|-
| [[ChEMBL]]
| [[EMBL-EBI]]
| 2009<ref>{{Cite web|url=https://www.ebi.ac.uk/chembl/|title = ChEMBL Database}}</ref>
|-
|Reaxys [https://www.elsevier.com/en-in/products/reaxys bioactivity] [[Reaxys|DB]]
|Elsevier
|2017
|-
| [[PubChem|PubChem-BioAssay]]
| [[NIH]] 
| 2004<ref>{{Cite web|url=https://pubchem.ncbi.nlm.nih.gov/|title=PubChem|website=pubchem.ncbi.nlm.nih.gov}}</ref><ref>{{cite journal| pmc=5210581 | pmid=27899599 | doi=10.1093/nar/gkw1118 | volume=45 | title=PubChem BioAssay: 2017 update | year=2017 | journal=Nucleic Acids Res | pages=D955–D963 | last1 = Wang | first1 = Y | last2 = Bryant | first2 = SH | last3 = Cheng | first3 = T | last4 = Wang | first4 = J | last5 = Gindulyte | first5 = A | last6 = Shoemaker | first6 = BA | last7 = Thiessen | first7 = PA | last8 = He | first8 = S | last9 = Zhang | first9 = J| issue=D1 }}</ref>
|-
|}

=== Chemical structures ===
[[Chemical structure]]s are traditionally represented using lines indicating [[chemical bonds]] between [[atoms]] and drawn on paper (2D [[structural formula]]e). While these are ideal visual representations for the [[chemist]], they are unsuitable for computational use and especially for [[search algorithm|search]] and [[computer storage|storage]]. Small molecules (also called [[ligands]] in drug design applications), are usually represented using lists of atoms and their connections. Large molecules such as proteins are however more compactly represented using the sequences of their amino acid building blocks. Radioactive isotopes are also represented, which is an important attribute for some applications. Large chemical databases for structures are expected to handle the storage and searching of information on millions of molecules taking [[terabytes]] of physical memory.<ref name=Hoffmann2019>{{cite journal |last1=Hoffmann |first1=Torsten |last2=Gastreich |first2=Marcus |title=The next level in chemical space navigation: going far beyond enumerable compound libraries |journal=Drug Discovery Today |volume=24 |issue=5 |date=2019 |doi=10.1016/j.drudis.2019.02.013 |doi-access=free |pages=1148–1156|pmid=30851414 }}</ref><ref>{{cite journal |doi=10.1038/s41586-023-05905-z |doi-access=free |title=Computational approaches streamlining drug discovery |date=2023 |last1=Sadybekov |first1=Anastasiia V. |last2=Katritch |first2=Vsevolod |journal=Nature |volume=616 |issue=7958 |pages=673–685 |pmid=37100941 |bibcode=2023Natur.616..673S }}</ref>

=== Literature database ===

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

=== Crystallographic database ===

[[Crystallographic databases]] store X-ray crystal structure data.  Common examples include [[Protein Data Bank]] and [[Cambridge Structural Database]].

=== NMR spectra database ===

[[NMR spectra database]]s correlate chemical structure with NMR data.  These databases often include other characterization data such as [[FTIR]] and [[mass spectrometry]].

=== Reactions database ===

Most chemical databases store information on [[chemical stability|stable]] [[molecule]]s but in databases for reactions also intermediates and temporarily created unstable molecules are stored. Reaction databases contain information about products, educts, and [[reaction mechanism]]s.

A popular example that lists [[chemical reaction]] data, among others, would be the [[Beilstein database]], [https://www.elsevier.com/en-in/products/reaxys Reaxys]

=== 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, [[Enthalpy of vaporization|vaporization]], and [[Enthalpy of fusion|fusion]].
* caloric data like [[heat capacity]], [[heat of formation]] and [[Heat of combustion|combustion]],
* transport properties like [[viscosity]] and [[thermal conductivity]]