ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation
Background Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial...
Gespeichert in:
| Veröffentlicht in: | Journal of cheminformatics 2015-12, Vol.7 (1), p.60-60 |
|---|---|
| Hauptverfasser: | , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 60 |
|---|---|
| container_issue | 1 |
| container_start_page | 60 |
| container_title | Journal of cheminformatics |
| container_volume | 7 |
| creator | Dong, Jie Cao, Dong-Sheng Miao, Hong-Yu Liu, Shao Deng, Bai-Chuan Yun, Yong-Huan Wang, Ning-Ning Lu, Ai-Ping Zeng, Wen-Bin Chen, Alex F. |
| description | Background
Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attempt to ease the process. However, there are still several hurdles for users to overcome to fully harness the power of these tools. First, most of the tools are distributed as standalone software or packages that require necessary configuration or programming efforts of users. Second, many of the tools can only calculate a subset of molecular descriptors, and the results from multiple tools need to be manually merged to generate a comprehensive set of descriptors. Third, some packages only provide application programming interfaces and are implemented in different computer languages, which pose additional challenges to the integration of these tools.
Results
A freely available web-based platform, named ChemDes, is developed in this study. It integrates multiple state-of-the-art packages (i.e., Pybel, CDK, RDKit, BlueDesc, Chemopy, PaDEL and jCompoundMapper) for computing molecular descriptors and fingerprints. ChemDes not only provides friendly web interfaces to relieve users from burdensome programming work, but also offers three useful and convenient auxiliary tools for format converting, MOPAC optimization and fingerprint similarity calculation. Currently, ChemDes has the capability of computing 3679 molecular descriptors and 59 types of molecular fingerprints.
Conclusion
ChemDes provides users an integrated and friendly tool to calculate various molecular descriptors and fingerprints. It is freely available at
http://www.scbdd.com/chemdes
. The source code of the project is also available as a supplementary file.
Graphical abstract:
An overview of ChemDes. A platform for computing various molecular descriptors and fingerprints |
| doi_str_mv | 10.1186/s13321-015-0109-z |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_proquest_miscellaneous_1837305133</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1749616601</sourcerecordid><originalsourceid>FETCH-LOGICAL-p245t-dce1af44c71a9b5746c11e675e8c208174454707a23037c7b2a412e1475d672a3</originalsourceid><addsrcrecordid>eNqFkU1LAzEQhoMotlZ_gBdZ8OJlNZPPrTepn1DwoldDNjutW_bLZBexv96UKhQvHjIZhoeXmfcl5BToJUCmrgJwziClIOOj03S9R8agZZayqVD7O_2IHIWwolRJTfUhGTGllBAyG5O32TvWtxiuE9skZdPj0tsei-QT8zS3IXZdZftF6-sklqRuK3RDZX1SYHC-7Po4tE2RLMpmib7zUSJxbd0Nve3LtjkmBwtbBTz5-Sfk9f7uZfaYzp8fnmY387RjQvZp4RDsQginwU5zqYVyAKi0xMwxmoGOy4q4umWccu10zqwAhiC0LJRmlk_IxVa38-3HgKE3dRkcVpVtsB2CgYxrTmX0639Ui6kCpShE9PwPumoH38RDoqCSkmeUbQTPfqghr7Ew0YTa-i_za3IE2BYIG3-iTTsy1GySNNskTUzSbJI0a_4NrvmNfQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1865538023</pqid></control><display><type>article</type><title>ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation</title><source>BioMedCentral</source><source>Springer Nature - Complete Springer Journals</source><source>DOAJ Directory of Open Access Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><source>PubMed Central Open Access</source><source>Springer Nature OA Free Journals</source><creator>Dong, Jie ; Cao, Dong-Sheng ; Miao, Hong-Yu ; Liu, Shao ; Deng, Bai-Chuan ; Yun, Yong-Huan ; Wang, Ning-Ning ; Lu, Ai-Ping ; Zeng, Wen-Bin ; Chen, Alex F.</creator><creatorcontrib>Dong, Jie ; Cao, Dong-Sheng ; Miao, Hong-Yu ; Liu, Shao ; Deng, Bai-Chuan ; Yun, Yong-Huan ; Wang, Ning-Ning ; Lu, Ai-Ping ; Zeng, Wen-Bin ; Chen, Alex F.</creatorcontrib><description>Background
Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attempt to ease the process. However, there are still several hurdles for users to overcome to fully harness the power of these tools. First, most of the tools are distributed as standalone software or packages that require necessary configuration or programming efforts of users. Second, many of the tools can only calculate a subset of molecular descriptors, and the results from multiple tools need to be manually merged to generate a comprehensive set of descriptors. Third, some packages only provide application programming interfaces and are implemented in different computer languages, which pose additional challenges to the integration of these tools.
Results
A freely available web-based platform, named ChemDes, is developed in this study. It integrates multiple state-of-the-art packages (i.e., Pybel, CDK, RDKit, BlueDesc, Chemopy, PaDEL and jCompoundMapper) for computing molecular descriptors and fingerprints. ChemDes not only provides friendly web interfaces to relieve users from burdensome programming work, but also offers three useful and convenient auxiliary tools for format converting, MOPAC optimization and fingerprint similarity calculation. Currently, ChemDes has the capability of computing 3679 molecular descriptors and 59 types of molecular fingerprints.
Conclusion
ChemDes provides users an integrated and friendly tool to calculate various molecular descriptors and fingerprints. It is freely available at
http://www.scbdd.com/chemdes
. The source code of the project is also available as a supplementary file.
Graphical abstract:
An overview of ChemDes. A platform for computing various molecular descriptors and fingerprints</description><identifier>ISSN: 1758-2946</identifier><identifier>EISSN: 1758-2946</identifier><identifier>DOI: 10.1186/s13321-015-0109-z</identifier><identifier>PMID: 26664458</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Chemistry ; Chemistry and Materials Science ; Computational Biology/Bioinformatics ; Computer Applications in Chemistry ; Documentation and Information in Chemistry ; Software ; Theoretical and Computational Chemistry</subject><ispartof>Journal of cheminformatics, 2015-12, Vol.7 (1), p.60-60</ispartof><rights>Dong et al. 2015</rights><rights>Journal of Cheminformatics is a copyright of Springer, 2015.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1186/s13321-015-0109-z$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1186/s13321-015-0109-z$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,860,27901,27902,41096,41464,42165,42533,51294,51551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26664458$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dong, Jie</creatorcontrib><creatorcontrib>Cao, Dong-Sheng</creatorcontrib><creatorcontrib>Miao, Hong-Yu</creatorcontrib><creatorcontrib>Liu, Shao</creatorcontrib><creatorcontrib>Deng, Bai-Chuan</creatorcontrib><creatorcontrib>Yun, Yong-Huan</creatorcontrib><creatorcontrib>Wang, Ning-Ning</creatorcontrib><creatorcontrib>Lu, Ai-Ping</creatorcontrib><creatorcontrib>Zeng, Wen-Bin</creatorcontrib><creatorcontrib>Chen, Alex F.</creatorcontrib><title>ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation</title><title>Journal of cheminformatics</title><addtitle>J Cheminform</addtitle><addtitle>J Cheminform</addtitle><description>Background
Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attempt to ease the process. However, there are still several hurdles for users to overcome to fully harness the power of these tools. First, most of the tools are distributed as standalone software or packages that require necessary configuration or programming efforts of users. Second, many of the tools can only calculate a subset of molecular descriptors, and the results from multiple tools need to be manually merged to generate a comprehensive set of descriptors. Third, some packages only provide application programming interfaces and are implemented in different computer languages, which pose additional challenges to the integration of these tools.
Results
A freely available web-based platform, named ChemDes, is developed in this study. It integrates multiple state-of-the-art packages (i.e., Pybel, CDK, RDKit, BlueDesc, Chemopy, PaDEL and jCompoundMapper) for computing molecular descriptors and fingerprints. ChemDes not only provides friendly web interfaces to relieve users from burdensome programming work, but also offers three useful and convenient auxiliary tools for format converting, MOPAC optimization and fingerprint similarity calculation. Currently, ChemDes has the capability of computing 3679 molecular descriptors and 59 types of molecular fingerprints.
Conclusion
ChemDes provides users an integrated and friendly tool to calculate various molecular descriptors and fingerprints. It is freely available at
http://www.scbdd.com/chemdes
. The source code of the project is also available as a supplementary file.
Graphical abstract:
An overview of ChemDes. A platform for computing various molecular descriptors and fingerprints</description><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>Software</subject><subject>Theoretical and Computational Chemistry</subject><issn>1758-2946</issn><issn>1758-2946</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkU1LAzEQhoMotlZ_gBdZ8OJlNZPPrTepn1DwoldDNjutW_bLZBexv96UKhQvHjIZhoeXmfcl5BToJUCmrgJwziClIOOj03S9R8agZZayqVD7O_2IHIWwolRJTfUhGTGllBAyG5O32TvWtxiuE9skZdPj0tsei-QT8zS3IXZdZftF6-sklqRuK3RDZX1SYHC-7Po4tE2RLMpmib7zUSJxbd0Nve3LtjkmBwtbBTz5-Sfk9f7uZfaYzp8fnmY387RjQvZp4RDsQginwU5zqYVyAKi0xMwxmoGOy4q4umWccu10zqwAhiC0LJRmlk_IxVa38-3HgKE3dRkcVpVtsB2CgYxrTmX0639Ui6kCpShE9PwPumoH38RDoqCSkmeUbQTPfqghr7Ew0YTa-i_za3IE2BYIG3-iTTsy1GySNNskTUzSbJI0a_4NrvmNfQ</recordid><startdate>20151209</startdate><enddate>20151209</enddate><creator>Dong, Jie</creator><creator>Cao, Dong-Sheng</creator><creator>Miao, Hong-Yu</creator><creator>Liu, Shao</creator><creator>Deng, Bai-Chuan</creator><creator>Yun, Yong-Huan</creator><creator>Wang, Ning-Ning</creator><creator>Lu, Ai-Ping</creator><creator>Zeng, Wen-Bin</creator><creator>Chen, Alex F.</creator><general>Springer International Publishing</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>NPM</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></search><sort><creationdate>20151209</creationdate><title>ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation</title><author>Dong, Jie ; Cao, Dong-Sheng ; Miao, Hong-Yu ; Liu, Shao ; Deng, Bai-Chuan ; Yun, Yong-Huan ; Wang, Ning-Ning ; Lu, Ai-Ping ; Zeng, Wen-Bin ; Chen, Alex F.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p245t-dce1af44c71a9b5746c11e675e8c208174454707a23037c7b2a412e1475d672a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><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>Software</topic><topic>Theoretical and Computational Chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dong, Jie</creatorcontrib><creatorcontrib>Cao, Dong-Sheng</creatorcontrib><creatorcontrib>Miao, Hong-Yu</creatorcontrib><creatorcontrib>Liu, Shao</creatorcontrib><creatorcontrib>Deng, Bai-Chuan</creatorcontrib><creatorcontrib>Yun, Yong-Huan</creatorcontrib><creatorcontrib>Wang, Ning-Ning</creatorcontrib><creatorcontrib>Lu, Ai-Ping</creatorcontrib><creatorcontrib>Zeng, Wen-Bin</creatorcontrib><creatorcontrib>Chen, Alex F.</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>PubMed</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Health & 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 & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</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 & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</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><jtitle>Journal of cheminformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dong, Jie</au><au>Cao, Dong-Sheng</au><au>Miao, Hong-Yu</au><au>Liu, Shao</au><au>Deng, Bai-Chuan</au><au>Yun, Yong-Huan</au><au>Wang, Ning-Ning</au><au>Lu, Ai-Ping</au><au>Zeng, Wen-Bin</au><au>Chen, Alex F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation</atitle><jtitle>Journal of cheminformatics</jtitle><stitle>J Cheminform</stitle><addtitle>J Cheminform</addtitle><date>2015-12-09</date><risdate>2015</risdate><volume>7</volume><issue>1</issue><spage>60</spage><epage>60</epage><pages>60-60</pages><issn>1758-2946</issn><eissn>1758-2946</eissn><abstract>Background
Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attempt to ease the process. However, there are still several hurdles for users to overcome to fully harness the power of these tools. First, most of the tools are distributed as standalone software or packages that require necessary configuration or programming efforts of users. Second, many of the tools can only calculate a subset of molecular descriptors, and the results from multiple tools need to be manually merged to generate a comprehensive set of descriptors. Third, some packages only provide application programming interfaces and are implemented in different computer languages, which pose additional challenges to the integration of these tools.
Results
A freely available web-based platform, named ChemDes, is developed in this study. It integrates multiple state-of-the-art packages (i.e., Pybel, CDK, RDKit, BlueDesc, Chemopy, PaDEL and jCompoundMapper) for computing molecular descriptors and fingerprints. ChemDes not only provides friendly web interfaces to relieve users from burdensome programming work, but also offers three useful and convenient auxiliary tools for format converting, MOPAC optimization and fingerprint similarity calculation. Currently, ChemDes has the capability of computing 3679 molecular descriptors and 59 types of molecular fingerprints.
Conclusion
ChemDes provides users an integrated and friendly tool to calculate various molecular descriptors and fingerprints. It is freely available at
http://www.scbdd.com/chemdes
. The source code of the project is also available as a supplementary file.
Graphical abstract:
An overview of ChemDes. A platform for computing various molecular descriptors and fingerprints</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>26664458</pmid><doi>10.1186/s13321-015-0109-z</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1758-2946 |
| ispartof | Journal of cheminformatics, 2015-12, Vol.7 (1), p.60-60 |
| issn | 1758-2946 1758-2946 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1837305133 |
| source | BioMedCentral; Springer Nature - Complete Springer Journals; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry; PubMed Central Open Access; Springer Nature OA Free Journals |
| subjects | Chemistry Chemistry and Materials Science Computational Biology/Bioinformatics Computer Applications in Chemistry Documentation and Information in Chemistry Software Theoretical and Computational Chemistry |
| title | ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-10T08%3A52%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=ChemDes:%20an%20integrated%20web-based%20platform%20for%20molecular%20descriptor%20and%20fingerprint%20computation&rft.jtitle=Journal%20of%20cheminformatics&rft.au=Dong,%20Jie&rft.date=2015-12-09&rft.volume=7&rft.issue=1&rft.spage=60&rft.epage=60&rft.pages=60-60&rft.issn=1758-2946&rft.eissn=1758-2946&rft_id=info:doi/10.1186/s13321-015-0109-z&rft_dat=%3Cproquest_pubme%3E1749616601%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1865538023&rft_id=info:pmid/26664458&rfr_iscdi=true |