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Encyclopedia > 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. Not to be confused with informatics or information theory. ... For other uses, see Chemistry (disambiguation). ... In Silico is a full length artist album by Deepsky View From a Stairway Jareths Church The Mansion World (Deepskys Trippin In Unknown Territory Mix) Ride Three Sheets to the Wind Atia Metro Smile Cosmic Dancer (2002 remix) Until the End of the World Let Me Live Categories... Pharmacology (in Greek: pharmacon is drug, and logos is science) is the study of how chemical substances interfere with living systems. ... In medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered and/or designed. ...

Contents

History

The term Chemoinformatics was defined by F.K. Brown [1][2] 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. [3]


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.[4][5] It is to be expected that the chemical space contains at least 1060 molecules. Cheminformatics can also be applied to data analysis for various industries like paper and pulp,dyes and such allied industries. For other uses, see Chemistry (disambiguation). ... Computer science, or computing science, is the study of the theoretical foundations of information and computation and their implementation and application in computer systems. ... Chemical space is the space spanned by all possible (i. ... Chemical space is the space spanned by all possible (i. ...


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: To meet Wikipedias content policies, the external links section for this article may require cleanup. ... Data mining is the principle of sorting through large amounts of data and picking out relevant information. ... As a broad subfield of artificial intelligence, 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. ...

Unstructured data refers to masses of (usually) computerized information which do not have a data structure which is easily readable by a machine. ... Structured data mining is the process of finding and extracting useful information from raw datasets. ... A binary tree, a simple type of branching linked data structure. ... Database mining is a special case of Structured Data Mining. ... Graph mining is a special case of Structured Data Mining. ... This page describes mining for molecules. ... Sequence mining or string mining is a special case of Structured Data Mining. ... Tree mining is a special case of Structured Data Mining. ...

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. This article discusses some common molecular file formats, including usage and converting between them. ... The Extensible Markup Language (XML) is a general-purpose markup language. ... CML (Chemical Markup Language) is a new approach to manage molecular information using tools such as XML and Java. ... The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. ... To meet Wikipedias content policies, the external links section for this article may require cleanup. ...


Virtual 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. It has been suggested that this article or section be merged with High-throughput_screening. ... High-throughput screening (HTS), is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology and chemistry. ... In Silico is a full length artist album by Deepsky View From a Stairway Jareths Church The Mansion World (Deepskys Trippin In Unknown Territory Mix) Ride Three Sheets to the Wind Atia Metro Smile Cosmic Dancer (2002 remix) Until the End of the World Let Me Live Categories... 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. ... Combinatorial chemistry involves the rapid synthesis or the computer simulation of a large number of different but structurally related molecules. ... Secondary metabolites, also known as natural products, are those products (chemical compounds) of metabolism that are not essential for normal growth, development or reproduction of an organism. ...


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. Quantitative structure-activity relationship (QSAR) is the process by which chemical structure is quantitatively correlated with a well defined process, such as biological activity or chemical reactivity. ... Quantitative structure-activity relationship (QSAR) is the process by which chemical structure is quantitatively correlated with a well defined process, such as biological activity or chemical reactivity. ... The Quantitative Structure Property Relationship (QSPR) is used in the field of chemistry, and relates bio-physico-chemical properties of chemical compounds to their structures. ... Chemometrics is the application of mathematical or statistical methods to chemical data. ... An expert system is a software system that attempts to reproduce the performance of one or more human experts, most commonly in a specific problem domain, and is a traditional application and/or subfield of artificial intelligence. ... In Silico is a full length artist album by Deepsky View From a Stairway Jareths Church The Mansion World (Deepskys Trippin In Unknown Territory Mix) Ride Three Sheets to the Wind Atia Metro Smile Cosmic Dancer (2002 remix) Until the End of the World Let Me Live Categories...


See also

Map of the human X chromosome (from the NCBI website). ... This article discusses some common molecular file formats, including usage and converting between them. ... Chemogenomics can be defined as a genomic response to chemical compounds. ... Computational chemistry is a branch of chemistry that uses the results of theoretical chemistry incorporated into efficient computer programs to calculate the structures and properties of molecules and solids, applying these programs to complement the information obtained by actual chemical experiments, predict hitherto unobserved chemical phenomena, and solve related problems. ... Combinatorial chemistry involves the rapid synthesis or the computer simulation of a large number of different but structurally related molecules. ... Data analysis is the act of transforming data with the aim of extracting useful information and facilitating conclusions. ... Chemometrics is the application of mathematical or statistical methods to chemical data. ... The Journal of Chemical Information and Modeling (usually abbreviated as , JCIM), is a peer-reviewed scientific journal, published since 1961 by the American Chemical Society. ... This page aims to list articles related to chemistry. ... 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. ... Mathematical chemistry is a branch of theoretical chemistry. ... The backbone dihedral angles are included in the molecular model of a protein. ... 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. ... A scientific visualization of an extremely large simulation of a Raleigh-Taylor instability caused by two mixing fluids. ... This article is about the field of statistics. ...

References

  1. ^ 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.
  2. ^ Brown, Frank. Editorial Opinion: Chemoinformatics – a ten year update Current Opinion in Drug Discovery & Development (2005), 8(3), 296-302.
  3. ^ Obernai Declaration
  4. ^ Gasteiger J.(Editor), Engel T.(Editor): Chemoinformatics : A Textbook. John Wiley & Sons, 2004, ISBN 3-527-30681-1
  5. ^ A.R. Leach, V.J. Gillet: An Introduction to Chemoinformatics. Springer, 2003, ISBN 1-4020-1347-7

External links

  • The Free On-line Cheminformatics Service
  • The Blue Obelisk Movement
  • The eCheminfo Network and Community of Practice
  • Cheminformatics at Indiana University
  • The Chemical Structure Association Trust (see also CSA Trust).
  • Comprehensive cheminformatics link list and data set repository
  • A cheminformatics glossary
  • Chemoinf.com Chemoinformatics Hub
  • moltable.org Chemoinformatics initiatives
  • Chemical Informatics Education and Research at Indiana University
  • Famous Cheminformatics quotations
  • The Cheminformatics and QSAR Society
  • UK-QSAR and ChemoInformatics Group
  • Education and Research at the University of Hamburg
  • Cheminformatics research at the Unilever Centre for Molecular Informatics, Cambridge, UK
By the mid 20th century humans had achieved a mastery of technology sufficient to leave the surface of the Earth for the first time and explore space. ... For the song by 311, see Grassroots Applied science is the exact science of applying knowledge from one or more natural scientific fields to practical problems. ... AI redirects here. ... Ceramic engineering is the technology of manufacturing and usage of ceramic materials. ... A processors core Computing is a very broad topic that has become pandemic to modern uses of technology. ... Surface mount electronic components Electronics is the study of the flow of charge through various materials and devices such as semiconductors, resistors, inductors, capacitors, nano-structures and vacuum tubes. ... Energy storage is the storing of some form of energy that can be drawn upon at a later time to perform some useful operation. ... Engineering physics (EP) is an academic degree, usually at the level of Bachelor of Science. ... 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Pharmacology (in Greek: pharmakon (φάρμακον) meaning drug, and lego (λέγω) to tell (about)) is the study of how drugs interact with living organisms to produce a change in function. ... Safety engineering is an applied science strongly related to systems engineering and the subset System Safety Engineering. ... Sanitary engineering is the application of scientific or mathematical principles with to the field of sanitation, especially in regards to its affect on public health. ... Look up aerospace in Wiktionary, the free dictionary. ... Aerospace engineering is the branch of engineering that concerns the design, construction and science behind aircraft and spacecraft. ... Automotive engineering is a branch of Vehicle engineering, incorporating elements of mechanical, electrical, electronic, software and safety engineering as applied to the design, manufacture and operation of automobiles, buses and trucks and their respective engineering subsystems. ... 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  Results from FactBites:
 
Cheminformatics - ChemicalInformationSources (391 words)
Cheminformatics is the application of information technology to the investigation of chemistry research problems and to the organization and analysis of chemical data.
Cheminformatics has had its biggest impact in the pharmaceutical industry, although its techniques and tools are beginning to be applied to other areas of chemistry.
In order for cheminformatics to succeed, certain standards had to be developed, although often a development of a dominant company turned into a standard coding method if made public, as in the case of MDL's SDF format or more recently, their CTfile format.
The Scientist : Cheminformatics: Redefining the Crucible (2033 words)
Cheminformatics used to be limited by processor speed, he says, but that is no longer the case.
Key areas in basic research where cheminformatics plays a pivotal role are the development of pharmacophore maps—descriptors that define the physical, chemical, and structural make-up of a compound with pharmaceutical potential—and the examination of macromolecule-small molecule interactions, such as receptor-ligand and enzyme-inhibitor/activator associations.
The ultimate goal of any cheminformatics system is to provide an integrated environment that conducts searches across multiple data types and dimensions, to find commonalities and relationships between the data, and to provide mechanisms to experiment with these findings in the virtual realm.
  More results at FactBites »

 
 

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