Cheminformatics

Information about Cheminformatics

Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can also be used in chemical and allied industries in various other forms.

History

The term (chemical) graph was introduced by Cullen in 1758.[1] He used those graphs for affinity diagrams showing a relationship between chemical substances. Those results have never been published officially.

The term Chemoinformatics was defined by F.K. Brown [2][3] in 1998:

Chemoinformatics is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization.


Since then, both spellings have been used, and some have evolved to be established as Cheminformatics [1], while European Academia settled in 2006 for Chemoinformatics. [4]

Basics

Cheminformatics combines the scientific working fields of chemistry and computer science for example in the area of chemical graph theory and mining the chemical space.[5][6] It is to be expected that the chemical space contains at least molecules. Cheminformatics can also applied to data analysis for various industries like paper and pulp,dyes and such allied industries.

Applications

Storage and retrieval

Main article: Chemical database
The primary application of cheminformatics is in the storage of information relating to compounds. The efficient search of such stored information includes topics that are dealt in computer science as data mining and machine learning. Related research topics include:

File formats

Main article: Chemical file format
The in silico representation of chemical structures uses specialized formats such as the XML-based Chemical Markup Language, or SMILES. These representations are often used for storage in large chemical databases. While some formats are suited for visual representations in 2 or 3 dimensions, others are more suited for studying physical interactions, modeling and docking studies.

Virtual screening

Main article: Virtual_high_throughput_screening
In contrast to high-throughput screening, virtual screening involves the creation of large in silico virtual libraries of compounds, which are then submitted to a docking program in order to identify the most active members. In some cases, combinatorial chemistry is used in the development of the library to increase the efficiency in mining the chemical space. More commonly, a diverse library of small molecules or natural products is screened.

Quantitative structure-activity relationship (QSAR)

Main article: Quantitative structure-activity relationship
This is the calculation of quantitative structure-activity relationship and quantitative structure property relationship values, used to predict the activity of compounds from their structures. In this context there is also a strong relationship to Chemometrics. Chemical expert systems are also relevant, since they represent parts of chemical knowledge as an in silico representation.

See also

References

1. ^ D. Bonchev, D.H. Rouvray: Chemical Graph Theory: Introduction and Fundamentals. Gordon and Breach Science Publishers, 1990, ISBN 0-85626-454-7.
2. ^ F.K. Brown Chapter 35. Chemoinformatics: What is it and How does it Impact Drug Discovery. Annual Reports in Med. Chem., Ed. James A. Bristol, 1998, Vol. 33, pp. 375.
3. ^ Brown, Frank. Editorial Opinion: Chemoinformatics – a ten year update Current Opinion in Drug Discovery & Development (2005), 8(3), 296-302.
4. ^ Obernai Declaration
5. ^ Gasteiger J.(Editor), Engel T.(Editor): Chemoinformatics : A Textbook. John Wiley & Sons, 2004, ISBN 3-527-30681-1
6. ^ A.R. Leach, V.J. Gillet: An Introduction to Chemoinformatics. Springer, 2003, ISBN 1-4020-1347-7

External links

Major fields of technology [ Edit]
Biomedical engineering | Biotechnology | Computer Science technology | Electrical engineering | Electronics | Energy | Energy storage | Gaming | Information technology | Machinery | Metallurgy | Microtechnology | Mining | Nanotechnology | Nuclear technology | Space technology | Telecommunication | Transport | Visual technology | Weapons technology
Information science (also information studies) is an interdisciplinary science primarily concerned with the collection, classification, manipulation, storage, retrieval and dissemination of information.
..... Click the link for more information.
Editing of this page by unregistered or newly registered users is currently disabled due to vandalism.
If you are prevented from editing this page, and you wish to make a change, please discuss changes on the talk page, request unprotection, log in, or .
..... Click the link for more information.
In Silico is a full length artist album by Deepsky

In Silico

Studio album by Deepsky
Released February 5, 2002
Genre Progressive electronic music
Label Kinetic Records

Track listing:

  1. "View From a Stairway"

..... Click the link for more information.
A pharmaceutical company, or drug company, is a commercial business whose focus is to research, develop, market and/or distribute drugs, most commonly in the context of healthcare. They can deal in generic and/or brand medications.
..... Click the link for more information.
In medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered and/or designed.

In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery.
..... Click the link for more information.
graph is a kind of data structure, specifically an abstract data type (ADT), that consists of a set of nodes and a set of edges that establish relationships (connections) between the nodes. The graph ADT follows directly from the graph concept from mathematics.
..... Click the link for more information.
Editing of this page by unregistered or newly registered users is currently disabled due to vandalism.
If you are prevented from editing this page, and you wish to make a change, please discuss changes on the talk page, request unprotection, log in, or .
..... Click the link for more information.
Computer science, or computing science, is the study of the theoretical foundations of information and computation and their implementation and application in computer systems.
..... Click the link for more information.
graph theory is the study of graphs; mathematical structures used to model pairwise relations between objects from a certain collection. A "graph" in this context refers to a collection of vertices or 'nodes' and a collection of edges
..... Click the link for more information.
Chemical space is the space spanned by all possible (i.e. energetically stable) stoichiometrical combinations of electrons and atomic nuclei and topologies (isomers) in molecules. Chemical reactions allow us to move in chemical space.
..... Click the link for more information.
Chemical space is the space spanned by all possible (i.e. energetically stable) stoichiometrical combinations of electrons and atomic nuclei and topologies (isomers) in molecules. Chemical reactions allow us to move in chemical space.
..... Click the link for more information.
A chemical database is a database specifically designed to store chemical information. Most chemical databases store information on stable molecules. Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D
..... Click the link for more information.
Data mining can be defined as "the nontrivial extraction of implicit, previously unknown, and potentially useful information from data".[1] Data mining may also be defined as "the science of extracting useful information from large data sets or databases".
..... Click the link for more information.
machine learning is concerned with the design and development of algorithms and techniques that allow computers to "learn". At a general level, there are two types of learning: inductive, and deductive.
..... Click the link for more information.
Unstructured data (or unstructured information) refers to masses of (usually) computerized information which do either not have a data structure or one that is not easily readable by a machine.
..... Click the link for more information.
Structured data mining is the process of finding and extracting useful information from raw datasets. This page may one day describe mining for general data structures. Graph mining is a special case of Structured Data Mining, which is related to Molecule mining.
..... Click the link for more information.
data structure is a way of storing data in a computer so that it can be used efficiently. Often a carefully chosen data structure will allow the most efficient algorithm to be used. The choice of the data structure often begins from the choice of an abstract data type.
..... Click the link for more information.
Structured data mining is the process of finding and extracting useful information from raw datasets. This page may one day describe mining for general data structures. Graph mining is a special case of Structured Data Mining, which is related to Molecule mining.
..... Click the link for more information.
Structured data mining is the process of finding and extracting useful information from raw datasets. This page may one day describe mining for general data structures. Graph mining is a special case of Structured Data Mining, which is related to Molecule mining.
..... Click the link for more information.
This page describes mining for molecules. Since molecules are multi-labeled graphs this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances.
..... Click the link for more information.
Sequence mining is concerned with finding statistically relevant patterns between data examples where the values are delivered in a sequence. It is usually presumed that the values are discrete, and thus Time series mining is closely related, but usually considered a different
..... Click the link for more information.
Structured data mining is the process of finding and extracting useful information from raw datasets. This page may one day describe mining for general data structures. Graph mining is a special case of Structured Data Mining, which is related to Molecule mining.
..... Click the link for more information.
Simplified Molecular Input Line Entry Specification]] (SMILES) is a line notation for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates.

Hydrogen atoms are not represented.
..... Click the link for more information.
Extensible Markup Language

File extension: .xml
MIME type: application/xml, text/xml (deprecated)
Uniform Type Identifier: public.xml
Developed by: World Wide Web Consortium
Type of format: Markup language
Extended from: SGML
..... Click the link for more information.
cml

File extension: .cml
Type of format: chemical file format

CML (Chemical Markup Language) is a new approach to managing molecular information using tools such as XML and Java.
..... Click the link for more information.
smiles

File extension: .smi
Type of format: chemical file format

The simplified molecular input line entry specification or SMILES
..... Click the link for more information.
A chemical database is a database specifically designed to store chemical information. Most chemical databases store information on stable molecules. Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D
..... Click the link for more information.
High-throughput screening (HTS), is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology and chemistry.

Purpose and method


..... Click the link for more information.
In Silico is a full length artist album by Deepsky

In Silico

Studio album by Deepsky
Released February 5, 2002
Genre Progressive electronic music
Label Kinetic Records

Track listing:

  1. "View From a Stairway"

..... Click the link for more information.
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.
..... Click the link for more information.

This article is copied from an article on Wikipedia.org - the free encyclopedia created and edited by online user community. The text was not checked or edited by anyone on our staff. Although the vast majority of the wikipedia encyclopedia articles provide accurate and timely information please do not assume the accuracy of any particular article. This article is distributed under the terms of GNU Free Documentation License.