Modular Chemical Descriptor Language (MCDL): Stereochemical modules

Background In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representati...

Full description

Saved in:
Bibliographic Details
Published in:Journal of cheminformatics 2011-01, Vol.3 (1), p.5-5, Article 5
Main Authors: Gakh, Andrei A, Burnett, Michael N, Trepalin, Sergei V, Yarkov, Alexander V
Format: Article
Language:English
Subjects:
ALGORITHMS
Chemistry
Chemistry and Materials Science
Computational Biology/Bioinformatics
Computer Applications in Chemistry
Documentation and Information in Chemistry
GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ISOMERS
JAVA
Methodology
Molecular structure
PROCESSING
Public software
Software
STEREOCHEMISTRY
STORAGE
TESTING
Theoretical and Computational Chemistry
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3
cites cdi_FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3
container_end_page 5
container_issue 1
container_start_page 5
container_title Journal of cheminformatics
container_volume 3
creator Gakh, Andrei A
Burnett, Michael N
Trepalin, Sergei V
Yarkov, Alexander V
description Background In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. Results In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Conclusions Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.
doi_str_mv 10.1186/1758-2946-3-5
format article
fullrecord <record><control><sourceid>gale_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_23e738e021c24e8aa0e048321469af32</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A249717336</galeid><doaj_id>oai_doaj_org_article_23e738e021c24e8aa0e048321469af32</doaj_id><sourcerecordid>A249717336</sourcerecordid><originalsourceid>FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3</originalsourceid><addsrcrecordid>eNp1kktv1DAQgCMEoqVw5IpWcAAOKX7ELw6Iasuj0lYcgLPltSdZV0m8tRMk_j0OaXe7oiiHJJ5vPs94XBTPMTrFWPJ3WDBZElXxkpbsQXG8-3945_uoeJLSFUKcCSQeF0cEE8GJIMfF8jK4sTVxsdxA561pF-eQbPTbIcTFyvTNaBpYvLlcnq_evl98HyBCsLdoN-VCelo8qk2b4NnN-6T4-fnTj-XXcvXty8XybFWuOVdDqSTDspIYKVtzwalyDqionZRrWDOFDUVEUUYFwtQCq8ER4ySrraOyIszRk-Ji9rpgrvQ2-s7E3zoYr_8uhNhoEwdvW9CEgqASEMGWVCCNQYAqSQmuuDI1Jdn1YXZtx3UHzkI_RNMeSA8jvd_oJvzSFFVEcZkFL2dBSIPXyfoB7MaGvgc7aIywJFRl6OMMrX34zy6HERs6PU1NT1PTVLOseH1TaAzXI6RBdz5ZaFvTQxiTloxyIaSg-4p25FUYY58nohUiDIuK8Qy9mqHG5GPyfR3yvnZS6jNSKYGzaKJO76Hy46bJhx5qn9cPEso5wcaQUoR61yNGerqn_3T14u7x7-jbi7mvIOVQ30DcN3O_8Q9kIO39</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>902517456</pqid></control><display><type>article</type><title>Modular Chemical Descriptor Language (MCDL): Stereochemical modules</title><source>Springer Nature - SpringerLink Journals - Fully Open Access </source><source>Publicly Available Content (ProQuest)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Gakh, Andrei A ; Burnett, Michael N ; Trepalin, Sergei V ; Yarkov, Alexander V</creator><creatorcontrib>Gakh, Andrei A ; Burnett, Michael N ; Trepalin, Sergei V ; Yarkov, Alexander V ; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><description>Background In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. Results In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Conclusions Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.</description><identifier>ISSN: 1758-2946</identifier><identifier>EISSN: 1758-2946</identifier><identifier>DOI: 10.1186/1758-2946-3-5</identifier><identifier>PMID: 21276272</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>ALGORITHMS ; Chemistry ; Chemistry and Materials Science ; Computational Biology/Bioinformatics ; Computer Applications in Chemistry ; Documentation and Information in Chemistry ; GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE ; ISOMERS ; JAVA ; Methodology ; Molecular structure ; PROCESSING ; Public software ; Software ; STEREOCHEMISTRY ; STORAGE ; TESTING ; Theoretical and Computational Chemistry</subject><ispartof>Journal of cheminformatics, 2011-01, Vol.3 (1), p.5-5, Article 5</ispartof><rights>Gakh et al; licensee Chemistry Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>COPYRIGHT 2011 BioMed Central Ltd.</rights><rights>2011 Gakh et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright ©2011 Gakh et al; licensee Chemistry Central Ltd. 2011 Gakh et al; licensee Chemistry Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3</citedby><cites>FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/902517456/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/902517456?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,25731,27901,27902,36989,36990,44566,53766,53768,74869</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21276272$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1018239$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Gakh, Andrei A</creatorcontrib><creatorcontrib>Burnett, Michael N</creatorcontrib><creatorcontrib>Trepalin, Sergei V</creatorcontrib><creatorcontrib>Yarkov, Alexander V</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Modular Chemical Descriptor Language (MCDL): Stereochemical modules</title><title>Journal of cheminformatics</title><addtitle>J Cheminform</addtitle><addtitle>J Cheminform</addtitle><description>Background In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. Results In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Conclusions Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.</description><subject>ALGORITHMS</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Computational Biology/Bioinformatics</subject><subject>Computer Applications in Chemistry</subject><subject>Documentation and Information in Chemistry</subject><subject>GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE</subject><subject>ISOMERS</subject><subject>JAVA</subject><subject>Methodology</subject><subject>Molecular structure</subject><subject>PROCESSING</subject><subject>Public software</subject><subject>Software</subject><subject>STEREOCHEMISTRY</subject><subject>STORAGE</subject><subject>TESTING</subject><subject>Theoretical and Computational Chemistry</subject><issn>1758-2946</issn><issn>1758-2946</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNp1kktv1DAQgCMEoqVw5IpWcAAOKX7ELw6Iasuj0lYcgLPltSdZV0m8tRMk_j0OaXe7oiiHJJ5vPs94XBTPMTrFWPJ3WDBZElXxkpbsQXG8-3945_uoeJLSFUKcCSQeF0cEE8GJIMfF8jK4sTVxsdxA561pF-eQbPTbIcTFyvTNaBpYvLlcnq_evl98HyBCsLdoN-VCelo8qk2b4NnN-6T4-fnTj-XXcvXty8XybFWuOVdDqSTDspIYKVtzwalyDqionZRrWDOFDUVEUUYFwtQCq8ER4ySrraOyIszRk-Ji9rpgrvQ2-s7E3zoYr_8uhNhoEwdvW9CEgqASEMGWVCCNQYAqSQmuuDI1Jdn1YXZtx3UHzkI_RNMeSA8jvd_oJvzSFFVEcZkFL2dBSIPXyfoB7MaGvgc7aIywJFRl6OMMrX34zy6HERs6PU1NT1PTVLOseH1TaAzXI6RBdz5ZaFvTQxiTloxyIaSg-4p25FUYY58nohUiDIuK8Qy9mqHG5GPyfR3yvnZS6jNSKYGzaKJO76Hy46bJhx5qn9cPEso5wcaQUoR61yNGerqn_3T14u7x7-jbi7mvIOVQ30DcN3O_8Q9kIO39</recordid><startdate>20110131</startdate><enddate>20110131</enddate><creator>Gakh, Andrei A</creator><creator>Burnett, Michael N</creator><creator>Trepalin, Sergei V</creator><creator>Yarkov, Alexander V</creator><general>Springer International Publishing</general><general>BioMed Central Ltd</general><general>Springer Nature B.V</general><general>BioMed Central</general><general>BMC</general><scope>C6C</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QO</scope><scope>7X7</scope><scope>7XB</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>LK8</scope><scope>M0S</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20110131</creationdate><title>Modular Chemical Descriptor Language (MCDL): Stereochemical modules</title><author>Gakh, Andrei A ; Burnett, Michael N ; Trepalin, Sergei V ; Yarkov, Alexander V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>ALGORITHMS</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Computational Biology/Bioinformatics</topic><topic>Computer Applications in Chemistry</topic><topic>Documentation and Information in Chemistry</topic><topic>GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE</topic><topic>ISOMERS</topic><topic>JAVA</topic><topic>Methodology</topic><topic>Molecular structure</topic><topic>PROCESSING</topic><topic>Public software</topic><topic>Software</topic><topic>STEREOCHEMISTRY</topic><topic>STORAGE</topic><topic>TESTING</topic><topic>Theoretical and Computational Chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gakh, Andrei A</creatorcontrib><creatorcontrib>Burnett, Michael N</creatorcontrib><creatorcontrib>Trepalin, Sergei V</creatorcontrib><creatorcontrib>Yarkov, Alexander V</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><collection>Springer Open Access</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Health &amp; Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science &amp; Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central</collection><collection>Advanced Technologies &amp; Aerospace Database‎ (1962 - current)</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Biological Sciences</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>ProQuest advanced technologies &amp; aerospace journals</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals (Open Access)</collection><jtitle>Journal of cheminformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gakh, Andrei A</au><au>Burnett, Michael N</au><au>Trepalin, Sergei V</au><au>Yarkov, Alexander V</au><aucorp>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Modular Chemical Descriptor Language (MCDL): Stereochemical modules</atitle><jtitle>Journal of cheminformatics</jtitle><stitle>J Cheminform</stitle><addtitle>J Cheminform</addtitle><date>2011-01-31</date><risdate>2011</risdate><volume>3</volume><issue>1</issue><spage>5</spage><epage>5</epage><pages>5-5</pages><artnum>5</artnum><issn>1758-2946</issn><eissn>1758-2946</eissn><abstract>Background In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. Results In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Conclusions Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>21276272</pmid><doi>10.1186/1758-2946-3-5</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1758-2946
ispartof Journal of cheminformatics, 2011-01, Vol.3 (1), p.5-5, Article 5
issn 1758-2946
1758-2946
language eng
recordid cdi_doaj_primary_oai_doaj_org_article_23e738e021c24e8aa0e048321469af32
source Springer Nature - SpringerLink Journals - Fully Open Access ; Publicly Available Content (ProQuest); PubMed Central; Free Full-Text Journals in Chemistry
subjects ALGORITHMS
Chemistry
Chemistry and Materials Science
Computational Biology/Bioinformatics
Computer Applications in Chemistry
Documentation and Information in Chemistry
GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ISOMERS
JAVA
Methodology
Molecular structure
PROCESSING
Public software
Software
STEREOCHEMISTRY
STORAGE
TESTING
Theoretical and Computational Chemistry
title Modular Chemical Descriptor Language (MCDL): Stereochemical modules
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-04T12%3A58%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Modular%20Chemical%20Descriptor%20Language%20(MCDL):%20Stereochemical%20modules&rft.jtitle=Journal%20of%20cheminformatics&rft.au=Gakh,%20Andrei%20A&rft.aucorp=Oak%20Ridge%20National%20Lab.%20(ORNL),%20Oak%20Ridge,%20TN%20(United%20States)&rft.date=2011-01-31&rft.volume=3&rft.issue=1&rft.spage=5&rft.epage=5&rft.pages=5-5&rft.artnum=5&rft.issn=1758-2946&rft.eissn=1758-2946&rft_id=info:doi/10.1186/1758-2946-3-5&rft_dat=%3Cgale_doaj_%3EA249717336%3C/gale_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-b669t-9851848109cf67639dde37fd88beb591a30293537013ce5fed2ad85fcd38425d3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=902517456&rft_id=info:pmid/21276272&rft_galeid=A249717336&rfr_iscdi=true