Cheminformatics also known as chemoinformatics and chemical informatics is the use of computer and Information science 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 ... as Cheminformatics, ref http www.molinspiration.com chemoinformatics.html Cheminformatics ... Declaration ref The recent establishment of the Journal of Cheminformatics is a strong push towards the shorter variant. Basics Cheminformatics combines the scientific working fields of chemistry and computer ... An Introduction to Chemoinformatics . Springer, 2003, ISBN 1 4020 1347 7 ref Cheminformatics can also ... data and databases The primary application of cheminformatics is in the storage, indexing and search ... References references External links http www.eyesopen.com oechem tk OEChem Cheminformatics Programming ... Network and Community of Practice http djwild.info ed Cheminformatics courses at Indiana University ... Indiana Cheminformatics Education Portal http reccr.chem.rpi.edu Cheminformatics at Rensselaer ... also CSA Trust . http www.cheminformatics.org Comprehensive cheminformatics link list and data set repository http www.genomicglossaries.com content chemoinformatics gloss.asp A cheminformatics glossary ... index.php Cheminformatics and mining quotation Cheminformatics quotations http www.qsar.org The Cheminformatics ... http www ucc.ch.cam.ac.uk Cheminformatics research at the Unilever Centre for Molecular Informatics ... Informatique d Avignon LIA, France http www.novamechanics.com Cheminformatics research at NovaMechanics Cyprus http www.qspr.pe.kr my index.php?option com bookmarks&Itemid 28 Weblink Cheminformatics SW and DB http chemoinformatician.co.uk Cheminformatics studies from Unilever Centre for Molecular ... footer Category Computational chemistry Category Cheminformatics Category Drug discovery Category ... Cheminformatics sr Heminformatika ta uk ... more details
OELib was an Open Source Cheminformatics library. Its actual GNU General Public License GPLed C and Java programming language Java successors are OpenBabel and JOELib . Its commercial successor is called OEChem. See also JOELib OpenBabel External links Archived copy of http web.archive.org web 20081006063616 http www.eyesopen.com products toolkits oelib.html OELib in 2008 on Internet Archive . http www.eyesopen.com products toolkits oechem.html OEChem Category Chemistry software Category Free science software Category Cheminformatics Soft eng stub ... more details
Infobox Journal title QSAR & Combinatorial Science cover discipline Cheminformatics , QSAR , Combinatorial chemistry language English abbreviation QSAR Comb. Sci. website http www3.interscience.wiley.com cgi bin jtoc 104557877 Content URL br http www3.interscience.wiley.com cgi bin jabout 104557877 2022 info.html Informational URL publisher John Wiley & Sons country United States USA history 1981 to present ISSN 1611 020X eISSN 1611 0218 The QSAR & Combinatorial Science usually abbreviated as QSAR Comb. Sci. , is a peer review ed scientific journal , published since 1981 by John Wiley & Sons . It was originally published as the Quantitative Structure Activity Relationships , but changed its name in 2003 to the current title. It is the official journal of The QSAR and Modelling Society and the Society of Combinatorial Sciences . See also Cheminformatics QSAR Combinatorial chemistry External links http www.ndsu.nodak.edu qsar soc The QSAR and Modelling Society http www.combichem.org Society of Combinatorial Sciences Category Chemistry journals Category Computer science journals Category Cheminformatics chem journal stub fr Molecular Informatics ... more details
Image JMEEditor2008 2.png thumb 250px JME Molecule Editor. The JME molecule editor Molecular Editor Ref Description is a Java Sun Java applet with which one can make and edit drawings, both of molecules and of reactions including generation of substructure queries , and can display molecules within an HTML page. The editor can generate Daylight SMILES or Chemical table file MDL Molfile s of the created structures. The JME Editor was written by Peter Ertl while at Comenius University and later at Novartis Ciba Geigy, Basel . It is available free for non commercial use and has become a standard for molecular structure input on the web. Ref Sites Ref Users See also Molecule editor Cheminformatics List of software for molecular mechanics modeling Software for molecular modeling External links http www.molinspiration.com jme index.html JME HomePage References Note Description http www.jcheminf.com content 2 1 1 P. Ertl, Molecular structure input on the web, J. Cheminformatics 2010, 2 1 Note Sites http peter ertl.com sites using jme editor.html Interesting cheminformatics services using the JME editor Note Users http www.molinspiration.com jme jmeusers.html List of institutions using the JME applet Category Freeware Category Computational chemistry software Category Cheminformatics chem stub science software stub tr JME ... more details
Primarysources date September 2008 CambridgeSoft was a cheminformatics software company based in Cambridge, Massachusetts , United States USA . The company was founded in 1986 by Stewart Rubenstein, then a graduate student in chemistry at Harvard University , and ended operations as an independent company in 2011. The historical main product is the molecule editor ChemDraw , often sold as part of the ChemOffice suite of programs. In 2011, CambridgeSoft was sold to PerkinElmer , a laboratory instruments company. External links http www.cambridgesoft.com CambridgeSoft homepage Category Companies based in Cambridge, Massachusetts ict company stub ... more details
Chemogenomics is the study of genomics genomic responses to chemical compound s. The goal is the rapid identification of novel drug s and drug target s, embracing multiple early phase drug development drug discovery technologies ranging from drug target identification target identification and drug target validation validation , through compound design and chemical synthesis , to biological testing and ADME profiling. See also Genomics Structural genomics Pharmacogenetics Pharmacogenomics Toxicogenomics Bioinformatics Cheminformatics Computational chemistry Molecular modelling QSAR Proteochemometrics References Chemogenomics in Drug Discovery A Medicinal Chemistry Perspective , H. Kubinyi Editor , G. M ller Editor , R. Mannhold Series Editor , G. Folkers Series Editor , Wiley VCH, 2004 .ISBN 3 527 30987 X External links http www.kubinyi.de dd 03.pdf Kubinyi s slides Medicinal chemistry genomics footer pharma stub Category Computational chemistry Category Genomics Category Omics Category Pharmacology Category Pharmaceutical industry Category Cheminformatics Ar de Chemische Genetik fr Chimiog nomique ko ... more details
Multiple issues advert December 2007 refimprove April 2007 Infobox Company company name ChemAxon company logo Image ChemAxon logo.png vector logo company type Private genre foundation 1998 founder location city location country location Budapest , Hungary origins area served industry Life Sciences , Information technology Informatics , Cheminformatics revenue operating income net income parent divisions subsid owner homepage http www.chemaxon.com www.chemaxon.com dissolved footnotes ChemAxon is a software company specializing in API application programming interfaces and End user computer science end user applications for cheminformatics and life science research. The company s main customer base consists of pharmaceutical , agrochemical and biotechnology companies, as well as Academia academic research groups and Third party software component third parties wishing to integrate cheminformatic functionalities in their products and services. ChemAxon Products include tools for visualization and drawing of molecules, chemical database searching and management, drug discovery. ChemAxon provides products free for academic use. Recent innovations Development of Markush structure storage and search capabilities without enumeration , with Markush structures from Thomson Reuters Derwent World Patents Index DWPISM database. http thomsonreuters.com content press room legal 376030 Partnership announcement sup 1 sup . See also Computational chemistry Cheminformatics Chemical database Drug design QSAR Data mining Molecule editor chemicalize.org References references 1. http thomsonreuters.com content press room legal 376030 Thomson Reuters Partnership announcement External links http www.chemaxon.com ChemAxon s official homepage http www.chemaxon.com demosite marvin index.html Marvin and Calculator Plugin online implementation Free structure drawing image generation and structure based predictions pKa, logP, logD, name structure, polar surface area PSA , H bond acceptor donor, c ... more details
In Computational complexity theory complexity theory , maximum common subgraph isomorphism MCS is an optimization problem that is known to be NP hard . The formal description of the problem is as follows Maximum common subgraph isomorphism G sub 1 sub , G sub 2 sub Input Two graph theory graph s G sub 1 sub and G sub 2 sub . Question What is the largest Glossary of graph theory Subgraphs induced subgraph of G sub 1 sub isomorphic to an induced subgraph of G sub 2 sub ? The associated decision problem , i.e., given G sub 1 sub , G sub 2 sub and an integer k , deciding whether G sub 1 sub contains an induced subgraph of at least k edges isomorphic to an induced subgraph of G sub 2 sub is NP complete . One possible solution for this problem is to build a Modular product of graphs modular product graph , in which the largest Clique problem clique represents a solution for the MCS problem. MCS algorithms have a long tradition in cheminformatics and Pharmacophore pharmacophore mapping . See also Graph isomorphism problem Subgraph isomorphism problem Molecule mining References cite book author Michael R. Garey and David S. Johnson year 1979 title Computers and Intractability A Guide to the Theory of NP Completeness publisher W.H. Freeman isbn 0 7167 1045 5 A1.4 GT48, pg.202. Category NP complete problems Category Cheminformatics Category Computational problems in graph theory ... more details
other applications with object oriented accessibility to a given set of capabilities. OEChem TK Cheminformatics ... Molecular modelling Cheminformatics Computational chemistry External links http www.eyesopen.com ... more details
Standards in chemistry The Blue Obelisk five years on journal Journal of Cheminformatics volume 3 year 2011 doi 10.1186 1758 2946 3 37 pmid 21999342 pmc 3205042 ref Multiple open source cheminformatics ... Obelisk Awards ref See also Cheminformatics References references External links official http www.blueobelisk.org Category Cheminformatics Category Free science software Category Open methodologies ... more details
Chemistry Central , launched August 22, 2006, ref cite web url http www.sciencebase.com science blog chemistry central.html title Next stop, Chemistry Central last Bradley first David date August 22, 2006 publisher Sciencebase accessdate 2009 07 31 ref is a for profit scientific publisher specializing in Open access publishing open access publication in chemistry. It is operated by BioMed Central and as such part of Springer Science Business Media . Publications Journal of Cheminformatics Chemistry Central Journal Notes references External links official http www.chemistrycentral.com publisher stub Category Open content publishers Category Chemistry journals Category Springer imprints ... more details
Infobox Journal title Journal of Chemical Information and Modeling cover image jcim cover.jpg editor William L. Jorgensen discipline Cheminformatics abbreviation J. Chem. Inf. Model. website http pubs.acs.org journals jcisd8 index.html publisher American Chemical Society country USA frequency Monthly history 1961 to present impact 3.882 impact year 2010 ISSN 1549 9596 eISSN 1520 5142 CODEN jcisd8 RSS http pubs.acs.org action showFeed?ui 0&mi qjmolc&ai 53h&jc jcisd8&type etoc&feed rss The Journal of Chemical Information and Modeling usually abbreviated as J. Chem. Inf. Model. , JCIM , is a peer review peer reviewed scientific journal , published since 1961 by the American Chemical Society . ref http pubs.acs.org American Chemical Society ref It was originally published as the Journal of Chemical Documentation JCD , but changed its name in 1975 to Journal of Chemical Information and Computer Sciences JCICS and again in 2005 to the current title. The impact factor of this journal is 3.882 2010 . ref Journal Citation Reports, 2009 ref JCIM is indexed in Chemical Abstracts Service CAS , SCOPUS , Proquest , British Library , PubMed , Web of Science , and SwetsWise. The current Editor is William L. Jorgensen . ref http pubs.acs.org page jcisd8 profile.html Editor profile ref References references Category Computer science journals Category Cheminformatics Category Computational chemistry Category American Chemical Society academic journals chem journal stub es Journal of Chemical Information and Modeling fr Journal of Chemical Information and Modeling ... more details
Image Polar surface area.png thumb 350px Polar surface area in red of paracetamol The polar surface area PSA of a molecule is defined as the surface sum over all polar atoms, primarily oxygen and nitrogen , also including their attached hydrogens. PSA is a commonly used medicinal chemistry metric for the optimisation of a drug s ability to permeate cells. Molecules with a polar surface area of greater than 140 angstrom s squared tend to be poor at permeating cell membranes. For molecules to penetrate the blood brain barrier and thus act on receptors in the central nervous system , a PSA less than 60 angstroms squared is usually needed. See also Lipinski s Rule of Five Biopharmaceutics Classification System Implicit solvation Cheminformatics Chemistry Development Kit JOELib References Ertl, P., Rohde, B., Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 2000 , 43 , 3714 3717. DOI 10.1021 jm000942e Ertl, P. http books.google.com books?id wEsxCtyUJUEC&printsec frontcover&cad 0 PPA111,M1 Polar Surface Area , in Molecular Drug Properties , R. Mannhold ed , Wiley VCH, pp. 111 126, 2007 External links http www.molinspiration.com cgi bin properties Interactive Polar Surface Area calculator http depth first.com articles 2007 09 19 easily calculate tpsa descriptors from smiles strings using ruby cdk Free, Programmable TPSA Calculator chem stub compsci stub Category Cheminformatics Category Medicinal chemistry zh ... more details
Infobox Company company name Chemical Computing Group company logo Image CCG logo.png Chemical Computing Group vector logo company type Private company Private genre foundation this parameter modifies Founded founder location city location country location Montreal , Quebec PQ , Canada origins key people area served industry Cheminformatics and bioinformatics software products MOE , PSILO revenue operating income net income num employees 30 parent divisions subsid owner company slogan homepage http www.chemcomp.com www.chemcomp.com dissolved footnotes Chemical Computing Group is a software company specializing in research software for computational chemistry , bioinformatics , cheminformatics , docking molecular docking , pharmacophore pharmacophore searching and molecular dynamics molecular simulation . The company s main customer base consists of pharmaceutical and biotechnology companies, as well as academia academic research groups. It is a private company that was founded in 1994 it is based in Montreal , Canada . Its main product, Molecular Operating Environment MOE , is written in a self contained programming system, the Scientific Vector Language SVL . Products http www.chemcomp.com software.htm MOE Molecular Operating Environment http www.chemcomp.com psilo info.htm PSILO A Protein Structure Database System Other institutions developing software for computational chemistry Accelrys Inte Ligand OpenEye Scientific Software Schr dinger company Schr dinger http www.vlifesciences.com VLifeMDS Software External links http www.chemcomp.com Chemical Computing Group official homepage http www.acscomp.org Awards CCG ccg.html Excellence Award for student posters at American Chemical Society ACS National Meetings http www.macresearch.org review moe molecular operating environment Review of MOE 2005.06 http www.genengnews.com articles chitem.aspx?aid 1443 Molecular fingerprints in MOE Discussion of Binary QSAR J rgen Bajorath 2004 , Chemoinformatics Concepts, Methods, a ... more details
Dynamic combinatorics combinatorial chemistry is defined as combinatorial chemistry under thermodynamic control. ref P.T. Corbett et al. Dynamic Combinatorial Chemistry Chem. Rev. 106 2006 3652 ref Introduction In a dynamic combinatorial library, all constituents are in equilibrium. The interconversion of library members into one another is through a reversible process that can involve covalent or non covalent interactions. The composition of the library is determined by the thermodynamic stability of each of the library members under the particular conditions of the experiment. ref P.T. Corbett et al. Dynamic Combinatorial Chemistry Chem. Rev. 106 2006 3652 ref Current Applications DCC is useful in identifying molecules with unusual binding properties, and provides synthetic routes to complex molecules that aren t easily accessible by other means. Amplification Active compounds of interest can be amplified by adding the target receptor to the reaction solution. The active compounds bind to the receptor compound, shifting the equilibrium position and allowing more of the active compound to be formed. Medicine and Pharmaceuticals drug delivery, synthetic receptors, biochem ligands, biosensors Materials smart materials Catalysis Empty section date January 2011 Foldamers Foldamers Self assembling molecules interlocking architectures and new soft materials Virtual Libraries and Molecular Modeling Empty section date July 2010 Prospects and Challenges Empty section date July 2010 See also Combinatorial chemistry Cheminformatics Drug discovery High throughput screening Mathematical chemistry Combinatorial biology References reflist External links DEFAULTSORT Dynamic Combinatorial Chemistry Category Cheminformatics Category Drug discovery Category Materials science chem stub ... more details
The Molecular Query Language MQL was designed to allow more complex, problem specific search methods in chemoinformatics . In contrast to the widely used Smiles arbitrary target specification SMARTS queries, MQL provides for the specification of spatial and physicochemical properties of atoms and bonds. Additionally, it can easily be extended to handle non atom based graphs, also known as reduced feature graphs. The query language is based on an extended Backus Naur form EBNF using JavaCC . See also Smiles arbitrary target specification SMARTS International Chemical Identifier References E. Proschak, J. K. Wegner, A. Schü ller, G. Schneider, U. Fechner, Molecular Query Language MQL A Context Free Grammar for Substructure Matching , J. Chem. Inf. Model., 2007 , 47 , 295 301. doi 10.1021 ci600305h External links http gecco.org.chemie.uni frankfurt.de mql Java Webstart application for MQL Query languages Category Cheminformatics ... more details
Orphan date April 2012 unreferenced date May 2011 Drug discovery and Drug development development requires the integration of multiple scientific and technological disciplines. These include chemistry , biology , pharmacology , pharmaceutical technology and extensive use of information technology . The latter is increasingly recognised as Pharmacoinformatics . Definition Pharmacoinformatics may be defined as Implementation and use of information technologies for the discovery and development of drugs as well as in pharmacy education . It sometimes is also referred as chembioinformatics. Introduction Main idea behind the field is to integrate plethora informatics branches viz chemoinformatics, bioinformatics, inmmunoinformatics etc. to single platform, resulting in seamless process of drug discovery. First dedicated department for Pharmacoinformatics was established at National Institute Of Pharmaceutical Education And Research, S.A.S. Nagar, India in 2003. Which is followed by different universities worldwide including a programme by European universities named European Pharmacoinformatics Initiative EuroPIN . Recently the University of Vienna established a http pharminfo.univie.ac.at Full Professorship for Pharmacoinformatics with Gerhard Ecker Gerhard F. Ecker as chair. Category Pharmacology Category Pharmaceutical industry Category Drug discovery Category Cheminformatics Category Bioinformatics ... more details
The Randi index , also known as the connectivity index , of a graph mathematics graph is the sum of bond contributions math 1 d i d j 1 2 math where math d i math and math d j math are the degrees of the vertices making bond i j . History This graph invariant was introduced by Milan Randi in 1975. ref citation first M. last Randi authorlink Milan Randi title Characterization of molecular branching journal Journal of the American Chemical Society volume 97 issue 23 year 1975 pages 6609 6615 doi 10.1021 ja00856a001 . ref It is often used in chemoinformatics for investigations of organic compound s. Notes reflist References Roberto Todeschini , Viviana Consonni 2009 Molecular Descriptors for Chemoinformatics , Wiley VCH , ISBN 978 3 527 31852 0 Category Graph invariants Category Mathematical chemistry Category Cheminformatics ru ... more details
Infobox Company company logo Image schrodinger.png frameless alt Schrodinger logo company name Schr dinger company type Private company Private foundation 1990 location New York City New York, NY, USA br Portland, Oregon Portland, OR, USA br Cambridge, Massachusetts Cambridge, MA, USA br San Diego, California San Diego, CA, USA br Rockville, Maryland Rockville, MD, USA br Bangalore, India br Tokyo, Japan br Mannheim Mannheim, Germany br Munich M nchen, Germany br Camberley Camberley, UK key people Ramy Farid, President br Murco Ringnalda, CFO br industry Computer software br Biotechnology br Cheminformatics br Bioinformatics br Life sciences br num employees 150 200 homepage URL www.schrodinger.com Schr dinger is a software company specializing in research software for computational chemistry , docking molecular docking , homology modeling , protein X ray crystallography Model building and phase refinement x ray crystallography refinement, bioinformatics , ADME prediction, cheminformatics , enterprise informatics, pharmacophore pharmacophore searching , molecular dynamics molecular simulation , and quantum mechanics . The company s main customer base consists of pharmaceutical and biotechnology companies, as well as academic and government research groups. Schr dinger also engages in drug discovery collaborations with pharmaceutical and biotechnology companies through its internal drug discovery group DDAG . Products BioLuminate Biologic medical product biologics modeling Canvas cheminformatics CombiGlide combinatorial ligand docking ConfGen conformation generation Core Hopping scaffold core hopping Desmond software Desmond molecular dynamics Epik Acid dissociation constant pKa prediction Glide docking molecular docking Induced Fit Induced fit Induced fit induced fit docking JAGUAR Jaguar quantum mechanics KNIME Extensions LigPrep 2D to 3D conversion MacroModel molecular mechanics Maestro molecular viewer and graphical interface Phase pharmacophore pharmacophore mod ... more details
Wiswesser Line Notation , also referred to as WLN , invented by William Wiswesser William J. Wiswesser in 1949, ref cite journal author William J. Wiswesser title How the WLN began in 1949 and how it might be in 1999 journal Journal of Chemical Information and Computer Sciences J. Chem. Inf. Comput. Sci. year 1982 volume 22 issue 2 pages pp 88 93 doi 10.1021 ci00034a005 ref was the first line notation capable of precisely describing complex molecule s. It was the basis of ICI Ltd s CROSSBOW database system developed in the late 1960 s. It was also the tool used to develop the CAOCI Commercially Available Organic Chemical Intermediates database, the datafile from which MDL s ACD file was developed. WLN is still being extensively used by BARK Information Services. Examples L66J BMR& DSWQ IN1&1 6 dimethylamino 4 phenylamino naphthalene 2 sulfonic acid ref cite web title WLN History of Chemical Nomenclature date October 15, 2003 url http www.dalkescientific.com writings diary archive 2003 10 15 WLN.html accessdate 2006 12 17 author Andrew Dalke ref References references External links http www.emolecules.com doc cheminformatics 101.htm http depth first.com articles 2007 07 20 everything old is new again wiswesser line notation wln Everything Old is New Again Wiswesser Line Notation WLN chemistry stub Category Chemical nomenclature Category Cheminformatics Category Encodings de Wiswesser Line Notation simple Wiswesser Line Notation ... more details
Infobox journal editor Charles L. Brooks III, Gernot Frenking, Shigeyoshi Sakaki, Peter R. Schreiner discipline Chemistry abbreviation J. Comput. Chem. website http onlinelibrary.wiley.com journal 10.1002 ISSN 1096 987X publisher John Wiley & Sons country history 1980 present frequency 16 year impact 3.769 impact year 2009 ISSN 0192 8651 eISSN 1096 987X CODEN JCCHDD LCCN 80643914 OCLC 05081734 The Journal of Computational Chemistry is a peer review peer reviewed scientific journal published since 1980 by John Wiley & Sons . It covers research, contemporary developments in theory and methodology, and applications in all areas of computational chemistry , including ab initio quantum chemistry methods and semi empirical quantum chemistry method semiempirical method s, density functional theory , molecular mechanics , molecular dynamics , statistical mechanics , cheminformatics , protein folding biomolecular structure prediction , molecular design, and bioinformatics . According to the Journal Citation Reports , the journal has a 2009 impact factor of 3.769, ranking it 26th out of 138 journals in the category Chemistry, Multidisciplinary . ref name WoS cite web url http isiwebofknowledge.com title Web of Science year 2011 accessdate 2011 06 03 ref References Reflist External links Official website http www3.interscience.wiley.com cgi bin jhome 33822 Category Chemistry journals Category Publications established in 1980 Category John Wiley & Sons academic journals Category English language journals fr Journal of Computational Chemistry ... more details
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