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 ... used, and some have evolved to be established as Cheminformatics, ref http www.molinspiration.com chemoinformatics.html Cheminformatics or Chemoinformatics ? Bot generated title ref while European Academia ... Obernai 20Declaration.pdf Obernai Declaration ref The recent establishment of the Journal of Cheminformatics is a strong push towards the shorter variant. Basics Cheminformatics combines the scientific ... 1347 7 ref Cheminformatics can also be applied to data analysis for various industries like paper ... Storage and retrieval main Chemical database The primary application of cheminformatics is in the storage ... External links http www.eyesopen.com oechem tk OEChem Cheminformatics Programming Toolkit The http ... of Practice http cheminfo.informatics.indiana.edu Cheminformatics at Indiana University http icep.wikispaces.com Indiana Cheminformatics Education Portal http reccr.chem.rpi.edu Cheminformatics ... see 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 ... at Indiana University Famous http joelib.sourceforge.net wiki index.php Cheminformatics and mining quotation Cheminformatics quotations http www.qsar.org The Cheminformatics and QSAR Society http www.ukqsar.org ...?language en Education and Research at the University of Hamburg http www ucc.ch.cam.ac.uk Cheminformatics ... 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 Informatics to OpenEye Technology footer Category Computational chemistry Category Cheminformatics Category Drug discovery Category ... 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 http www.eyesopen.com products toolkits oelib.html OELib http www.eyesopen.com products toolkits oechem.html OEChem Category Chemistry software Category Free science software Category Cheminformatics Soft eng stub ... 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
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
. http www.eyesopen.com products toolkits oechem.html OEChem TK Cheminformatics and 3D molecular ... with OEChem. http www.eyesopen.com products toolkits cheminformatics toolkits.html ... cheminformatics toolkits.html MolProp TK 2D molecular property calculation and filtering. http www.eyesopen.com products toolkits cheminformatics toolkits.html Lexichem TK State of the art compound ... toolkits cheminformatics toolkits.html Ogham TK Elegant 2D structure rendering of compounds ... Chemical Computing Group See also Anthony Nicholls chemist Anthony Nicholls Molecular modelling Cheminformatics ... 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
Infobox Company company name iChemLabs LLC. company logo company type Private company Private foundation 2007 location city Piscataway, NJ location country USA location Piscataway , New Jersey NJ , USA area served Global industry Cheminformatics , Chemical Graphics homepage http www.ichemlabs.com www.ichemlabs.com iChemLabs iChemLabs LLC., develops desktop and web based scientific solutions, specializing in graphics and informatics. History iChemLabs was founded in February 2007 by Kevin Theisen to distribute the scientific software he was developing. He initially studied and developed algorithms to simulate nuclear magnetic resonance spectroscopy. This research involved the production of scientifically oriented graphical user interfaces, and his interests expanded to incorporate scientific visualization and graphics. iChemLabs is the developer of ChemDoodle and numerous other cheminformatics applications. Their goal is to support all operating systems including Linux, all web browsers for our web technologies, and all platforms including netbooks and mobile devices. Products ChemDoodle Desktop chemical publishing software ChemDoodle is a popular chemistry desktop software. ChemDoodle is a chemical structure environment with a main focus on 2D graphics and publishing to create media for your structures, reactions and spectra. ChemDoodle Web Components HTML5 cheminformatics and chemical graphics library The ChemDoodle Web Components library is a pure Javascript chemical graphics and cheminformatics library derived from the ChemDoodle application. ChemDoodle Web Components allow the wielder to present publication quality 2D and 3D graphics and animations for chemical structures, reactions and spectra. Beyond graphics, this tool provides a framework for user interaction to create dynamic applications through web browsers, desktop platforms and mobile devices such as the iPhone, iPad and Android devices. The goal of the project is to utilize HTML5 technologies to power ... more details
Infobox organization name Blue Obelisk image image border size alt caption map msize malt mcaption abbreviation motto formation 2005 extinction type status purpose headquarters location region served membership language leader title leader name main organ parent organization affiliations num staff num volunteers budget website http www.blueobelisk.org remarks Blue Obelisk is an informal group of chemists who promote Open Data , Open Source , and Open Standards it was initiated by Peter Murray Rust and others in 2005. ref The Blue Obelisk, Chemistry Development Kit CDK News CDK News , 2005, 2, 43&ndash 46 ref ref cite journal last1 Guha first1 R last2 Howard first2 MT last3 Hutchison first3 GR last4 Murray Rust first4 P last5 Rzepa first5 H last6 Steinbeck first6 C last7 Wegner first7 J last8 Willighagen first8 EL title The Blue Obelisk interoperability in chemical informatics journal Journal of chemical information and modeling volume 46 issue 3 pages 991 8 year 2006 pmid 16711717 doi 10.1021 ci050400b ref Multiple open source cheminformatics associate themselves with the Blue Obelisk, among which, in alphabetical order, Bioclipse , Chemistry Development Kit , JChemPaint , JOELib , Kalzium , Openbabel , http www.opensmiles.org OpenSMILES , and http usefulchem.wikispaces.com UsefulChem . The project has handed out personal awards for achievements in promoting Open Data, Open Source and Open Standards. Among those who received a Blue Obelisk Award are Christoph Steinbeck 2006 , Geoff Hutchinson 2006 , Bob Hanson 2006 , Egon Willighagen 2007 , Jean Claude Bradley 2007 , Ola Spjuth 2007 , Noel O Boyle 2010 , Rajarshi Guha 2010 , Cameron Neylon 2010 , Alex Wade 2010 , Nina Jeliazkova 2010 , Henry Rzepa 2011 , and Dan Zaharevitz 2011 . ref http blueobelisk.sourceforge.net wiki Blue Obelisk Awards ref See also Cheminformatics References references External links official http www.blueobelisk.org Category Cheminformatics Category Free science software ... more details
Primarysources date September 2008 CambridgeSoft , based in Cambridge, Massachusetts , United States USA , is a cheminformatics software and Consultant consulting company. The company was founded in 1986 by Stewart Rubenstein, then a graduate student in chemistry at Harvard University , and has since remained independent. The company s historical main product is the molecule editor ChemDraw as part of the ChemOffice suite of programs. Today the company s growth is driven primarily through enterprise life science solutions, particularly electronic notebooks, chemical registration, screening biology, inventory, and scientific content. Consulting practice areas include knowledge management and Intellectual property IP protection, materials management, manufacturing, biological assay data systems, biological process, and chemical discovery information management and analysis. External links http www.cambridgesoft.com CambridgeSoft homepage Category Companies based in Cambridge, Massachusetts ict company stub ... more details
The Molecular Query Language MQL was designed for allowing more complex and problem specific search methods in chemoinformatics . The query language is based on an extended Backus Naur form EBNF using JavaCC . In contrast to Smiles arbitrary target specification SMARTS queries this allows the specification of spatial and physicochemical properties of atoms and bonds. Furthermore can it be easily extended to non atom based graphs, called reduced feature graphs. 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 Category Cheminformatics ... more details
Italic title The Journal of Computational Chemistry is a peer review peer reviewed scientific journal , published since 1980 by John Wiley & Sons . It publishes original research, contemporary developments in theory and methodology, and state of the art applications in all areas of computational chemistry , including ab initio quantum chemistry methods and semiempirical method s, density functional theory , molecular mechanics , molecular dynamics , statistical mechanics , cheminformatics , protein folding biomolecular structure prediction , molecular design, and bioinformatics . Each volume comprises 16 issues one volume is published per year. According to the Journal Citation Reports , the journal s 2009 impact factor is 3.769. External links Official 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 chem journal stub fr Journal of Computational Chemistry ... 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 abbreviated as J Cheminf ref http www.jcheminf.com info about ref is an open access journal that started in 2009, published by Chemistry Central. The current editors are Christoph Steinbeck and David Wild. ref http www.jcheminf.com edboard ref Chemistry Central Journal Notes references publisher stub Category Open content publishers Category Chemistry journals ... more details
The European chemical Substances Information System ESIS is the information system on chemicals of the European Union maintained by the European Chemicals Bureau . It provides access to several registers and lists EINECS European Inventory of Existing Commercial chemical Substances ELINCS European List of Notified Chemical Substances NLP No Longer Polymers BPD Biocide Biocidal Products Directive PBT Persistent, Bioaccumulative and Toxic C&L Classification and Labelling Export and Import of Dangerous Chemicals HPVCs High Production Volume Chemicals and LPVCs Low Production Volume Chemicals IUCLID Chemical Data Sheets Priority Lists, Risk Assessment process and tracking system External links http ecb.jrc.ec.europa.eu esis ESIS Category Cheminformatics de European chemical Substances Information System nl European chemical Substances Information System pl European chemical Substances Information System ... 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
unreferenced date April 2011 The InChI Trust is a not for profit organisation which promotes and improves the International Chemical Identifier standard for describing chemical substances. History and current status The InChI Trust was formed in 2009, and was granted charitable status in 2010. The Trust s Project Director is Steve Heller. Continuing development Scientific direction of the InChI standard is carried out by the IUPAC Division VIII Subcommittee, and funding of subgroups investigating and defining the expansion of the standard is carried out by both IUPAC and the InChI Trust. The InChI Trust funds the development, testing and documentation of the InChI. Current extensions are being defined to handle polymers and mixtures, Markush structures, reactions and organometallics, and once accepted by the Division VIII Subcommittee will be added to the algorithm. See also International Chemical Identifier Links http www.inchi trust.org InChI Trust site Category Chemical nomenclature Category Chemical file formats Category Cheminformatics Category Identifiers ... 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 Subgraph 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
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 Flag USA frequency Monthly history 1961 to present impact 3.882 impact year 2009 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 2009 . 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 is defined as the surface sum over all polar atoms, usually oxygen and nitrogen , including also attached hydrogens. PSA is a commonly used medicinal chemistry metric for the optimisation of cell permeability. Molecules with a polar surface area of greater than 140 angstrom s squared are usually believed to be poor at permeating cell membranes. For molecules to penetrate the blood brain barrier and thus acting on receptors in the central nervous system , PSA should be less than 60 angstrom s squared. 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 SVL Scientific Vector Language SVL . Products Molecular Operating Environment MOE PSILO Other institutions developing software for computational chemistry Accelrys Inte Ligand OpenEye Scientific Software 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, and Tools for Drug Discovery page 92 ISBN 978 1588292612 Category Research support companies Category Software companies of Canada Catego ... 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. 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
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