Chemical database

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

Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D structural formulae). While these are ideal visual representations for the chemist, they are unsuitable for computational use and especially for search and 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.{{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 }}{{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 }}

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

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

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.

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 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 capacity, heat of formation and combustion,
• transport properties like viscosity and thermal conductivity

There are two principal techniques for representing chemical structures in digital databases

• 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 depth first or breadth first traversal, such as:
• :SMILES/SMARTS, SLN, WLN, InChI

These approaches have been refined to allow representation of stereochemical differences and charges as well as special kinds of bonding such as those seen in organo-metallic compounds. The principal advantage of a computer representation is the possibility for increased storage and fast, flexible search.

{{Main|Substructure search}}

File:Lenalidomide substructures.svg 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.{{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 }}{{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 }}{{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 }}

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 at double bonds is catered for by giving a choice of retrieving only the E form, the Z form, or both.{{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}}

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,{{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 }}{{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}}{{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}} special function representations, moments of inertia, ray-tracing histograms, maximum distance histograms, shape multipoles to name a few.{{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}}{{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 }}{{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}}{{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}}{{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 }}

Large databases, such as PubChem{{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 }} and ChemSpider,{{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 }} have 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.{{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 }} PATENTSCOPE makes chemical patents accessible by substructure{{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 }} and Wikipedia's articles describing individual chemicals can also be searched that way.{{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 }}

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.{{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 }}{{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 }}

All properties of molecules beyond their structure can be split up into either physico-chemical or pharmacological attributes also called descriptors. On top of that, there exist various artificial and more or less standardized naming systems for molecules that supply more or less ambiguous names and synonyms. The IUPAC name is usually a good choice for representing a molecule's structure in a both human-readable and unique string although it becomes unwieldy for larger molecules. Trivial names on the other hand abound with homonyms and synonyms and are therefore a bad choice as a defining database key. While physico-chemical descriptors like molecular weight, (partial) charge, solubility, etc. can mostly be computed directly based on the molecule's structure, pharmacological descriptors can be derived only indirectly using involved multivariate statistics or experimental (screening, bioassay) results. All of those descriptors can for reasons of computational effort be stored along with the molecule's representation and usually are.

{{Main|Chemical similarity}}

There is no single definition of molecular similarity, however the concept may be defined according to the application and is often described as an inverse of a measure of distance in descriptor space. Two molecules might be considered more similar for instance if their difference in molecular weights is lower than when compared with others. A variety of other measures could be combined to produce a multi-variate distance measure. Distance measures are often classified into Euclidean measures and non-Euclidean measures depending on whether the triangle inequality holds. Maximum Common Subgraph (MCS) based substructure search {{cite journal|first1=S. A. |last1=Rahman|first2= M. |last2=Bashton |first3= G. L. |last3= Holliday |first4= R. |last4=Schrader |first5=J. M. |last5=Thornton |year=2000 |title=Small Molecule Subgraph Detector (SMSD) toolkit|journal= Journal of Cheminformatics|volume=1|issue=1|page=12|doi=10.1186/1758-2946-1-12|pmid=20298518|pmc=2820491 |doi-access=free }}(similarity or distance measure) is also very common. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).{{cite journal|first1=S. Asad |last1=Rahman|first2= M. |last2=Bashton|first3= G. L. |last3=Holliday|first4= R. |last4=Schrader |first5=J. M. |last5=Thornton|title= Small Molecule Subgraph Detector (SMSD) Toolkit|journal= Journal of Cheminformatics |year=2009|volume= 1|issue=1|page=12 |doi=10.1186/1758-2946-1-12 |pmid=20298518|pmc=2820491|url=http://www.ebi.ac.uk/thornton-srv/software/SMSD/ |doi-access=free }}

Chemicals in the databases may be clustered into groups of 'similar' molecules based on similarities. Both hierarchical and non-hierarchical clustering approaches can be applied to chemical entities with multiple attributes. These attributes or molecular properties may either be determined empirically or computationally derived descriptors. One of the most popular clustering approaches is the Jarvis-Patrick algorithm.{{cite journal|last=Butina|first= Darko |year=1999|title= Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets|journal= Chem. Inf. Comput. Sci. |volume=39|issue= 4 |pages=747–750|doi=10.1021/ci9803381}}

In pharmacologically oriented chemical repositories, similarity is usually defined in terms of the biological effects of compounds (ADME/tox) that can in turn be semiautomatically inferred from similar combinations of physico-chemical descriptors using QSAR methods.

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/'canonical' string representations such as 'canonical SMILES'. Some registration systems such as the CAS system make use of algorithms to generate unique hash codes to achieve the same objective.

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 stereochemistry unspecified, whereas a chemical registry system requires the registrar to specify whether the stereo configuration is unknown, a specific (known) mixture, or racemic. Each of these would be considered a different record in a chemical registry system.

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

An example is the Chemical Abstracts Service (CAS) registration system. See also CAS registry number.

• Accord
• Direct {{Cite web|url=https://www.3ds.com/products-services/biovia/products/scientific-informatics/biovia-direct/|title = BIOVIA Direct - BIOVIA - Dassault Systèmes®| date=8 September 2023 }}
• J Chem {{Cite web|url=https://chemaxon.com/products/jchem-engines|title = JChem Engines | ChemAxon}}
• CambridgeSoft {{Cite web|url=http://insideinformatics.cambridgesoft.com/categories/chemistry/oraclecartridge/default.aspx|title = Chemistry – Oracle Cartridge | Inside Informatics}}
• Bingo {{Cite journal|pmc = 2867114|year = 2010|last1 = Pavlov|first1 = D.|last2 = Rybalkin|first2 = M.|last3 = Karulin|first3 = B.|title = Bingo from SciTouch LLC: Chemistry cartridge for Oracle database|journal = Journal of Cheminformatics|volume = 2|issue = Suppl 1|pages = F1|doi = 10.1186/1758-2946-2-S1-F1 | doi-access=free }}
• Pinpoint {{Cite web|url=https://www.dotmatics.com/solutions/small-molecule-discovery|title=Small Molecule Drug Discovery Software|website=Small Molecule Drug Discovery Software}}

• ChemReg {{Cite web|url=https://www.3ds.com/products-services/biovia/products/laboratory-informatics/materials-management/biovia-registration/biovia-chemical-registration/|title=BIOVIA Chemical Registration - BIOVIA - Dassault Systèmes®|website=www.3ds.com|date=7 September 2023 }}
• Register{{Cite web|url=https://www.dotmatics.com/register|title=Register|access-date=2021-03-13|archive-date=2021-12-10|archive-url=https://web.archive.org/web/20211210205814/https://www.dotmatics.com/register|url-status=dead}}
• RegMol {{Cite web|url=https://www.scilligence.com/web/scilligence-regmol/|archive-url=https://web.archive.org/web/20180929130145/http://www.scilligence.com/web/scilligence-regmol/|url-status=dead|archive-date=September 29, 2018|title=Scilligence RegMol | Scilligence|date=6 June 2016}}
• Compound-Registration {{Cite web|url=https://chemaxon.com/compound-registration|title=Compound Registration|website=chemaxon.com}}
• Ensemble {{Cite web|url=https://perkinelmerinformatics.com/products/research/signals-notebook-eln|title=Signals Notebook - PerkinElmer Informatics|website=perkinelmerinformatics.com}}

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 OpenBabel. These search and conversion algorithms are implemented either within the database system itself or as is now the trend is implemented as external components that fit into standard relational database systems. Both Oracle and PostgreSQL based systems make use of cartridge technology that allows user defined datatypes. These allow the user to make SQL queries with chemical search conditions (For example, a query to search for records having a phenyl ring in their structure represented as a SMILES string in a SMILESCOL column could be

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

Algorithms for the conversion of IUPAC names to structure representations and vice versa are also used for extracting structural information from text. However, there are difficulties due to the existence of multiple dialects of IUPAC. Work is on to establish a unique IUPAC standard (See InChI).

• {{annotated link|Biological database}}
• [https://www.elsevier.com/en-in/products/reaxys Reaxys]- chemical and drug development database from Elsevier
• [https://www.elsevier.com/en-in/products/embiology Embiology] - biological relationship and target database
• [https://www.elsevier.com/en-in/products/pharmapendium Pharmapendium] - drug information
• {{annotated link|BindingDB}}
• {{annotated link|ChEBI}}
• {{annotated link|ChEMBL}}
• {{annotated link|Chemical similarity}}
• {{annotated link|Chemisches Zentralblatt|Chemisches Zentralblatt Structural Database}}
• {{annotated link|Collaborative Drug Discovery}}
• {{annotated link|Colocalization Benchmark Source}}
• {{annotated link|Comparative Toxicogenomics Database}}
• {{annotated link|Computational Chemistry List}}
• {{annotated link|DrugBank}}
• {{annotated link|List of chemical databases}}
• {{annotated link|List of software for molecular mechanics modeling}}
• {{annotated link|LOLI Database}}
• {{annotated link|NMR spectra database}}
• {{annotated link|Similarity search}}
• {{annotated link|SPRESI database}}

{{Reflist|2}}47. https://www.elsevier.com/en-in/products/reaxys

• [https://wikipedia.cheminfo.org/# Wikipedia Chemical Structure Explorer] to search Wikipedia chemistry articles by substructure

{{DEFAULTSORT:Chemical Database}}

Category:Computational chemistry

Category:Cheminformatics