Editing Chemical database (section)

== Search ==

=== Substructure ===
{{Main|Substructure search}}
[[File:Lenalidomide substructures.svg|thumb|The drug [[lenalidomide]] contains substructures [[isoindoline]] (red) and [[glutarimide]] (blue)]]
Chemists can search databases using parts of structures, parts of their [[IUPAC]] names as well as based on constraints on properties. Chemical databases are different from other general purpose databases in their support for substructure search, a method to retrieve chemicals matching a pattern of atoms and bonds which a user specifies. This kind of search is achieved by looking for [[subgraph isomorphism]] (sometimes also called a [[monomorphism]]) and is a widely studied application of [[graph theory]].<ref name=Currano>{{cite book |doi=10.1039/9781782620655-00109  |chapter=Chapter 5. Searching by Structure and Substructure |title=Chemical Information for Chemists |date=2014 |last1=Currano |first1=Judith N. |pages=109–145 |isbn=978-1-84973-551-3 }}</ref><ref name=Ullmann>{{cite journal |doi=10.1145/321921.321925 |doi-access=free |title=An Algorithm for Subgraph Isomorphism |date=1976 |last1=Ullmann |first1=J. R. |journal=[[Journal of the ACM]] |volume=23 |pages=31–42 }}</ref><ref name=Warr2011>{{cite journal |doi=10.1002/wcms.36 |title=Representation of chemical structures |date=2011 |last1=Warr |first1=Wendy A. |journal=WIREs Computational Molecular Science |volume=1 |issue=4 |pages=557–579 }}</ref>

Query structures may contain bonding patterns such as "single/aromatic" or "any" to provide flexibility. Similarly, the vertices which in an actual compound would be a specific atom may be replaced with an atom list in the query. [[Cis–trans isomerism|''Cis''–''trans'' isomerism]] at [[double bond]]s is catered for by giving a choice of retrieving only the [[E–Z notation|E form]], the [[E–Z notation|Z form]], or both.<ref name=Currano/><ref name=Pubchem>{{cite web |url=https://pubchem.ncbi.nlm.nih.gov/search/help_search.html |title=PubChem Structure Search |website=pubchem.ncbi.nlm.nih.gov |access-date=2024-08-01}}</ref>

===Conformation===
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]],<ref>{{cite journal|author1=Pearlman, R.S. |author2=Smith, K.M.|title=Metric Validation and the Receptor-Relevant Subspace Concept|journal=J. Chem. Inf. Comput. Sci.|year=1999|volume=39|pages=28–35|doi=10.1021/ci980137x }}</ref><ref name="q243">{{cite web | title=BCUTDescriptor (cdk 2.5 API) | website=CDK - Chemistry Development Kit | date=2021-05-05 | url=https://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.html | access-date=2024-06-04}}</ref><ref>{{cite journal |last1=Burden |first1=Frank R. |title=Molecular identification number for substructure searches |journal=Journal of Chemical Information and Computer Sciences |date=1 August 1989 |volume=29 |issue=3 |pages=225–227 |doi=10.1021/ci00063a011}}</ref> special function representations, [[moments of inertia]], [[Ray tracing (graphics)|ray-tracing]] histograms, maximum distance histograms, shape [[Fast multipole method|multipoles]] to name a few.<ref>{{cite journal|last1=Pearlman|first1= R.S. |last2=Smith |first2= K.M.|title= Metric Validation and the Receptor-Relevant Subspace Concept|journal= J. Chem. Inf. Comput. Sci.|year= 1999|volume= 39|pages=28–35|doi=10.1021/ci980137x}}</ref><ref>{{cite journal| last1=Lin, Jr.|first1=Hung |last2=Clark |first2= Timothy |year=2005|title= An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties|journal=  Journal of Chemical Information and Modeling|volume= 45|issue= 4|pages= 1010–1016|doi=10.1021/ci050059v|pmid=16045295 }}</ref><ref>{{cite journal|last1=Meek |first1=P. J.|last2= Liu|first2= Z.|last3= Tian|first3= L.|last4= Wang |first4=C. J|last5= Welsh |first5=W. J|last6= Zauhar|first6= R. J |year=2006|title= Shape Signatures: speeding up computer aided drug discovery|journal= DDT 2006 |volume=19–20|issue=19–20|pages=895–904|doi=10.1016/j.drudis.2006.08.014|pmid=16997139}}</ref><ref>{{cite journal|last1=Grant|first1= J. A|last2= Gallardo|first2= M. A.|last3= Pickup |first3=B. T. |year=1996|title= A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape |journal= Journal of Computational Chemistry|volume=17|issue= 14 |pages= 1653–1666|doi=10.1002/(sici)1096-987x(19961115)17:14<1653::aid-jcc7>3.0.co;2-k|s2cid= 96794688}}</ref><ref>{{cite journal|last1=Ballester|first1= P. J. |first2= W. G. |last2=Richards |year=2007 |title= Ultrafast shape recognition for similarity search in molecular databases|journal= [[Proceedings of the Royal Society A]] |volume= 463|issue= 2081 |pages=1307–1321|doi=10.1098/rspa.2007.1823|bibcode=2007RSPSA.463.1307B|s2cid= 12540483 }}</ref>

===Examples===
Large databases, such as [[PubChem]]<ref name=Pubchem/><ref>{{cite journal |doi=10.1002/cpz1.217 |title=Exploring Chemical Information in PubChem |date=2021 |last1=Kim |first1=Sunghwan |journal=Current Protocols |volume=1 |issue=8 |pages=e217 |pmid=34370395 |pmc=8363119 }}</ref> and [[ChemSpider]],<ref>{{cite book |doi=10.1021/bk-2010-1060.ch002 |chapter=ChemSpider: Integrating Structure-Based Resources Distributed across the Internet |title=Enhancing Learning with Online Resources, Social Networking, and Digital Libraries |series=ACS Symposium Series |date=2010 |last1=Williams |first1=Antony J. |volume=1060 |pages=23–39 |isbn=978-0-8412-2600-5 }}</ref> have [[graphical user interface|graphical interfaces]] for search. The [[Chemical Abstracts Service]] provides tools to search the chemical literature and [[Reaxys]] supplied by [[Elsevier]] covers both chemicals and reaction information, including that originally held in the [[Beilstein database]].<ref>{{cite journal |doi=10.1021/acs.jchemed.9b00966 |title=Property Information in Substance Records in Major Web-Based Chemical Information and Data Retrieval Tools: Understanding Content, Search Opportunities, and Application to Teaching |date=2020 |last1=Jarabak |first1=Charlotte |last2=Mutton |first2=Troy |last3=Ridley |first3=Damon D. |journal=Journal of Chemical Education |volume=97 |issue=5 |pages=1345–1359 |bibcode=2020JChEd..97.1345J }}</ref> [[Patentscope|PATENTSCOPE]] makes chemical patents accessible by substructure<ref>{{Cite web |title=Substructure Search Now Available in PATENTSCOPE |url=https://www.wipo.int/patentscope/en/news/pctdb/2019/news_0001.html |date=2019-02-11 |access-date=2024-08-04 |website=www.wipo.int }}</ref> and Wikipedia's articles describing individual chemicals can also be searched that way.<ref>{{cite journal |doi=10.1186/s13321-015-0061-y |doi-access=free |title=Wikipedia Chemical Structure Explorer: Substructure and similarity searching of molecules from Wikipedia |date=2015 |last1=Ertl |first1=Peter |last2=Patiny |first2=Luc |last3=Sander |first3=Thomas |last4=Rufener |first4=Christian |last5=Zasso |first5=Michaël |display-authors=3 |journal=Journal of Cheminformatics |volume=7 |page=10 |pmid=25815062 |pmc=4374119 }}</ref>

Suppliers of chemicals as synthesis intermediates or for [[high-throughput screening]] routinely provide search interfaces. Currently, the largest database that can be freely searched by the public is the [[ZINC database]], which is claimed to contain over 37 billion commercially available molecules.<ref name=ZINC>{{cite journal |doi=10.1021/acs.jcim.2c01253 |doi-access=free |title=ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery |date=2023 |last1=Tingle |first1=Benjamin I. |last2=Tang |first2=Khanh G. |last3=Castanon |first3=Mar |last4=Gutierrez |first4=John J. |last5=Khurelbaatar |first5=Munkhzul |last6=Dandarchuluun |first6=Chinzorig |last7=Moroz |first7=Yurii S. |last8=Irwin |first8=John J. |journal=Journal of Chemical Information and Modeling |volume=63 |issue=4 |pages=1166–1176 |pmid=36790087 |pmc=9976280 }}</ref><ref>{{cite journal |doi=10.1021/acs.jcim.2c00224 |title=Exploration of Ultralarge Compound Collections for Drug Discovery |date=2022 |last1=Warr |first1=Wendy A. |last2=Nicklaus |first2=Marc C. |last3=Nicolaou |first3=Christos A. |last4=Rarey |first4=Matthias |journal=Journal of Chemical Information and Modeling |volume=62 |issue=9 |pages=2021–2034 |pmid=35421301 }}</ref>