BoBER: web interface to the base of bioisosterically exchangeable replacements
Abstract We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioisosterism and scaffold hopping are key concepts in drug design and optimization, and...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2017-12-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13321-017-0251-x |
| _version_ | 1818063999301844992 |
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| author | Samo Lešnik Blaž Škrlj Nika Eržen Urban Bren Stanislav Gobec Janez Konc Dušanka Janežič |
| author_facet | Samo Lešnik Blaž Škrlj Nika Eržen Urban Bren Stanislav Gobec Janez Konc Dušanka Janežič |
| author_sort | Samo Lešnik |
| collection | DOAJ |
| description | Abstract We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioisosterism and scaffold hopping are key concepts in drug design and optimization, and can be defined as replacements of biologically active compound’s fragments with other fragments to improve activity, reduce toxicity, change bioavailability or to diversify the scaffold space. Our web server enables fast and user-friendly searches for bioisosteric and scaffold replacements which were obtained by mining the whole Protein Data Bank. The working of the web server is presented on an existing MurF inhibitor as example. BoBER web server enables medicinal chemists to quickly search for and get new and unique ideas about possible bioisosteric or scaffold hopping replacements that could be used to improve hit or lead drug-like compounds. |
| first_indexed | 2024-12-10T14:29:01Z |
| format | Article |
| id | doaj.art-37ac38fc940c45648545cf1badf8de04 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-10T14:29:01Z |
| publishDate | 2017-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-37ac38fc940c45648545cf1badf8de042022-12-22T01:44:58ZengBMCJournal of Cheminformatics1758-29462017-12-01911810.1186/s13321-017-0251-xBoBER: web interface to the base of bioisosterically exchangeable replacementsSamo Lešnik0Blaž Škrlj1Nika Eržen2Urban Bren3Stanislav Gobec4Janez Konc5Dušanka Janežič6National Institute of ChemistryNational Institute of ChemistryNational Institute of ChemistryNational Institute of ChemistryFaculty of Pharmacy, University of LjubljanaNational Institute of ChemistryFaculty of Mathematics, Natural Sciences and Information Technologies, University of PrimorskaAbstract We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioisosterism and scaffold hopping are key concepts in drug design and optimization, and can be defined as replacements of biologically active compound’s fragments with other fragments to improve activity, reduce toxicity, change bioavailability or to diversify the scaffold space. Our web server enables fast and user-friendly searches for bioisosteric and scaffold replacements which were obtained by mining the whole Protein Data Bank. The working of the web server is presented on an existing MurF inhibitor as example. BoBER web server enables medicinal chemists to quickly search for and get new and unique ideas about possible bioisosteric or scaffold hopping replacements that could be used to improve hit or lead drug-like compounds.http://link.springer.com/article/10.1186/s13321-017-0251-xProBiSProtein superimpositionBioisosteresScaffold hoppingLigand fragments |
| spellingShingle | Samo Lešnik Blaž Škrlj Nika Eržen Urban Bren Stanislav Gobec Janez Konc Dušanka Janežič BoBER: web interface to the base of bioisosterically exchangeable replacements Journal of Cheminformatics ProBiS Protein superimposition Bioisosteres Scaffold hopping Ligand fragments |
| title | BoBER: web interface to the base of bioisosterically exchangeable replacements |
| title_full | BoBER: web interface to the base of bioisosterically exchangeable replacements |
| title_fullStr | BoBER: web interface to the base of bioisosterically exchangeable replacements |
| title_full_unstemmed | BoBER: web interface to the base of bioisosterically exchangeable replacements |
| title_short | BoBER: web interface to the base of bioisosterically exchangeable replacements |
| title_sort | bober web interface to the base of bioisosterically exchangeable replacements |
| topic | ProBiS Protein superimposition Bioisosteres Scaffold hopping Ligand fragments |
| url | http://link.springer.com/article/10.1186/s13321-017-0251-x |
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