LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters
From the historically grown archive of protein−ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand−receptor interaction are derived from each of these s...
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| Veröffentlicht in: | Journal of chemical information and modeling 2005-01, Vol.45 (1), p.160-169 |
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| container_title | Journal of chemical information and modeling |
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| creator | Wolber, Gerhard Langer, Thierry |
| description | From the historically grown archive of protein−ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand−receptor interaction are derived from each of these small molecules and its surrounding amino acids. Based on a defined set of only six types of chemical features and volume constraints, three-dimensional pharmacophore models are constructed, which are sufficiently selective to identify the described binding mode and are thus a useful tool for in-silico screening of large compound databases. The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example. |
| doi_str_mv | 10.1021/ci049885e |
| format | Article |
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The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example.</description><identifier>ISSN: 1549-9596</identifier><identifier>EISSN: 1549-960X</identifier><identifier>DOI: 10.1021/ci049885e</identifier><identifier>PMID: 15667141</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Algorithms ; Antineoplastic Agents - chemistry ; Antineoplastic Agents - pharmacology ; Antiviral Agents - chemistry ; Antiviral Agents - pharmacology ; Binding sites ; Chemical compounds ; Computer based modeling ; Drug Design ; Fusion Proteins, bcr-abl ; Hydrogen Bonding ; Ligands ; Models, Chemical ; Models, Molecular ; Molecular Conformation ; Pharmacology ; Protein Binding ; Protein-Tyrosine Kinases - antagonists & inhibitors ; Rhinovirus - drug effects ; Software</subject><ispartof>Journal of chemical information and modeling, 2005-01, Vol.45 (1), p.160-169</ispartof><rights>Copyright © 2005 American Chemical Society</rights><rights>Copyright American Chemical Society Jan/Feb 2005</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a378t-b3c0aa4b0a38289a09ccd65801aa43ac03452f9b8570b3e17a1584cab878aca23</citedby><cites>FETCH-LOGICAL-a378t-b3c0aa4b0a38289a09ccd65801aa43ac03452f9b8570b3e17a1584cab878aca23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/ci049885e$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/ci049885e$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,777,781,2753,27058,27906,27907,56720,56770</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15667141$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wolber, Gerhard</creatorcontrib><creatorcontrib>Langer, Thierry</creatorcontrib><title>LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters</title><title>Journal of chemical information and modeling</title><addtitle>J. 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The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example.</description><subject>Algorithms</subject><subject>Antineoplastic Agents - chemistry</subject><subject>Antineoplastic Agents - pharmacology</subject><subject>Antiviral Agents - chemistry</subject><subject>Antiviral Agents - pharmacology</subject><subject>Binding sites</subject><subject>Chemical compounds</subject><subject>Computer based modeling</subject><subject>Drug Design</subject><subject>Fusion Proteins, bcr-abl</subject><subject>Hydrogen Bonding</subject><subject>Ligands</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular Conformation</subject><subject>Pharmacology</subject><subject>Protein Binding</subject><subject>Protein-Tyrosine Kinases - antagonists & inhibitors</subject><subject>Rhinovirus - drug effects</subject><subject>Software</subject><issn>1549-9596</issn><issn>1549-960X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpl0c1u1DAQB3ALgWgpHHgBZCFRiUPAjuOP9Fa2FJAWsWK3CHGxJs5s120Sb-0Ewa3XviZPQlCWVoKLbdk_j__yEPKUs1ec5fy186wojZF4j-xzWZRZqdjX-3_XslR75FFKF4wJUar8IdnjUinNC75PtnN_Dl29dGHoj35d31CRndDFBmILLmw3IWKiJxj9d6zpOoaWLmLo0XfZmzB0NZ1uJzoOdLVBH-lZQgqJfvGxH6ChSxcRO9-d01Pf9BjTY_JgDU3CJ7v5gJydvl3N3mfzT-8-zI7nGQht-qwSjgEUFQNhclMCK52rlTSMj7sCHBOFzNdlZaRmlUCugUtTOKiMNuAgFwfkcKq7jeFqwNTb1ieHTQMdhiFZpYWWiusRPv8HXoQhdmM2m3OVC6O1HNHLCbkYUoq4ttvoW4g_LWf2Tw_sbQ9G-2xXcKharO_k7tNHkE3Apx5_3J5DvJxS2dViab99_sgKNjd2NvoXkweX7sL9__BvPLGczQ</recordid><startdate>20050101</startdate><enddate>20050101</enddate><creator>Wolber, Gerhard</creator><creator>Langer, Thierry</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SC</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>7X8</scope></search><sort><creationdate>20050101</creationdate><title>LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters</title><author>Wolber, Gerhard ; Langer, Thierry</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a378t-b3c0aa4b0a38289a09ccd65801aa43ac03452f9b8570b3e17a1584cab878aca23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Algorithms</topic><topic>Antineoplastic Agents - chemistry</topic><topic>Antineoplastic Agents - pharmacology</topic><topic>Antiviral Agents - chemistry</topic><topic>Antiviral Agents - pharmacology</topic><topic>Binding sites</topic><topic>Chemical compounds</topic><topic>Computer based modeling</topic><topic>Drug Design</topic><topic>Fusion Proteins, bcr-abl</topic><topic>Hydrogen Bonding</topic><topic>Ligands</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular Conformation</topic><topic>Pharmacology</topic><topic>Protein Binding</topic><topic>Protein-Tyrosine Kinases - antagonists & inhibitors</topic><topic>Rhinovirus - drug effects</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wolber, Gerhard</creatorcontrib><creatorcontrib>Langer, Thierry</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Computer and Information Systems Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of chemical information and modeling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wolber, Gerhard</au><au>Langer, Thierry</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters</atitle><jtitle>Journal of chemical information and modeling</jtitle><addtitle>J. Chem. Inf. Model</addtitle><date>2005-01-01</date><risdate>2005</risdate><volume>45</volume><issue>1</issue><spage>160</spage><epage>169</epage><pages>160-169</pages><issn>1549-9596</issn><eissn>1549-960X</eissn><abstract>From the historically grown archive of protein−ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand−receptor interaction are derived from each of these small molecules and its surrounding amino acids. Based on a defined set of only six types of chemical features and volume constraints, three-dimensional pharmacophore models are constructed, which are sufficiently selective to identify the described binding mode and are thus a useful tool for in-silico screening of large compound databases. 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| fulltext | fulltext |
| identifier | ISSN: 1549-9596 |
| ispartof | Journal of chemical information and modeling, 2005-01, Vol.45 (1), p.160-169 |
| issn | 1549-9596 1549-960X |
| language | eng |
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| source | MEDLINE; ACS Publications |
| subjects | Algorithms Antineoplastic Agents - chemistry Antineoplastic Agents - pharmacology Antiviral Agents - chemistry Antiviral Agents - pharmacology Binding sites Chemical compounds Computer based modeling Drug Design Fusion Proteins, bcr-abl Hydrogen Bonding Ligands Models, Chemical Models, Molecular Molecular Conformation Pharmacology Protein Binding Protein-Tyrosine Kinases - antagonists & inhibitors Rhinovirus - drug effects Software |
| title | LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters |
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