Using Spherical Harmonic Surface Property Representations for Ligand‐Based Virtual Screening
Identifieur interne : 002652 ( Main/Merge ); précédent : 002651; suivant : 002653Using Spherical Harmonic Surface Property Representations for Ligand‐Based Virtual Screening
Auteurs : Violeta I. Pérez-Nueno [France, Allemagne] ; Vishwesh Venkatraman [France] ; Lazaros Mavridis [France] ; Tim Clark [Allemagne] ; David W. Ritchie [France]Source :
- Molecular Informatics [ 1868-1743 ] ; 2011-03-14.
English descriptors
- Teeft :
- Active ligands, Analogue bias, Binding pocket, Case study, Centre, Centre conf, Centre molecule, Chem, Chemical information, Compound level, Conf, Conformation, Conformational level, Consensus, Consensus cluster, Consensus conf, Consensus conformation, Consensus molecule, Consensus properties, Consensus shape, Consensus shape approach, Conventional queries, Crystal query, Crystal structure, Crystallographic query, Database, Different queries, Different ways, Difficult targets, Early performance, Early recognition, Early recognition performance, Enrichment factor, Expansion order, First stage, Flexible ligands, Full paper violeta, Genetic algorithm, Gmbh, Initial query compounds, Kgaa, Large number, Ligand, Local properties, Local surface properties, Molecule, Multiple ligands, Overall performance, Parafit, Parafit_bound parafit_rcm parafit_cm, Property representations, Query, Query conformation, Query conformations, Query optimization, Real centre molecule, Relative success, Results show, Rocs query, Rotatable bonds, Screening, Screening performance, Second stage, Surface properties, Surface property representations, Surface shape, Surface shapes, Verlag, Verlag gmbh, Virtual screening, Weighted properties, Weinheim.
- mix :
Abstract
Ligand‐based virtual screening (VS) techniques have become well established in the drug discovery process. However, despite their relative success, there still exists the problem of how to define the initial query compounds and which of their conformations should be used. Here, we propose a novel shape plus surface property approach using multiple local spherical harmonic (SH) functions. We also investigate the use of shape‐based and shape plus property‐based consensus SH queries calculated in several different ways. The utility of these approaches is compared using the 40 pharmaceutically relevant targets of the DUD database. Our results show that using a combination of SH‐based properties often gives better VS performance than using simple shape‐based queries. Shape‐based consensus queries also perform well, but we find that explicit 3D shape‐property conformations should be retained for highly flexible ligands.
Url:
DOI: 10.1002/minf.201000149
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ISTEX:328759D58EA3960AE5933ED4FD47E234F87B4F02Le document en format XML
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However, despite their relative success, there still exists the problem of how to define the initial query compounds and which of their conformations should be used. Here, we propose a novel shape plus surface property approach using multiple local spherical harmonic (SH) functions. We also investigate the use of shape‐based and shape plus property‐based consensus SH queries calculated in several different ways. The utility of these approaches is compared using the 40 pharmaceutically relevant targets of the DUD database. Our results show that using a combination of SH‐based properties often gives better VS performance than using simple shape‐based queries. 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last="Clark">Tim Clark</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-136577" status="INCOMING"><orgName>Computer Chimie Centrum,</orgName><orgName type="acronym">CCC</orgName><desc><address><country key="DE"></country></address></desc><listRelation><relation active="#struct-311714" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-311714" type="direct"><org type="institution" xml:id="struct-311714" status="VALID"><orgName>Friedrich-Alexander Universität Erlangen-Nürnberg</orgName><orgName type="acronym">FAU</orgName><desc><address><addrLine>Schlossplatz 491054 ErlangenGermany</addrLine><country key="DE"></country></address><ref type="url">http://www.fau.eu/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>Allemagne</country></affiliation></author><author><name sortKey="Ritchie, David" sort="Ritchie, David" uniqKey="Ritchie D" first="David" last="Ritchie">David Ritchie</name><affiliation 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Applications</orgName><orgName type="acronym">LORIA</orgName><desc><address><addrLine>Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.loria.fr</ref></desc><listRelation><relation name="UMR7503" active="#struct-441569" type="direct"></relation><relation active="#struct-300009" type="direct"></relation><relation active="#struct-300291" type="direct"></relation><relation active="#struct-300292" type="direct"></relation><relation active="#struct-300293" type="direct"></relation></listRelation></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-300291" type="indirect"><org type="institution" xml:id="struct-300291" status="OLD"><orgName>Université Henri Poincaré - Nancy 1</orgName><orgName type="acronym">UHP</orgName><date type="end">2011-12-31</date><desc><address><addrLine>24-30 rue Lionnois, BP 60120, 54 003 NANCY cedex, France</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-300292" type="indirect"><org type="institution" xml:id="struct-300292" status="OLD"><orgName>Université Nancy 2</orgName><date type="end">2011-12-31</date><desc><address><addrLine>91 avenue de la Libération, BP 454, 54001 Nancy cedex</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-300293" type="indirect"><org type="institution" xml:id="struct-300293" status="OLD"><orgName>Institut National Polytechnique de Lorraine</orgName><orgName type="acronym">INPL</orgName><date type="end">2011-12-31</date><desc><address><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-2496" type="direct"><org type="laboratory" xml:id="struct-2496" status="OLD"><orgName>INRIA Lorraine</orgName><desc><address><addrLine>615 rue du Jardin Botanique 54600 Villers-lès-Nancy</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/centre-de-recherche-inria/nancy-grand-est</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université Nancy 2</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Institut national polytechnique de Lorraine</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName></affiliation></author></analytic><idno type="DOI">10.1002/minf.201000149</idno><series><title level="j">Molecular Informatics</title><idno type="ISSN">1868-1743</idno><imprint><date type="datePub">2010-12-22</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Consensus properties</term><term>Difficult targets</term><term>FXA</term><term>Genetic algorithm</term><term>P38</term><term>PPAR-g</term><term>Spherical harmonics</term><term>Virtual screening</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ligand-based virtual screening (VS) techniques have become well established in the drug discovery process. However, despite their relative success, there still exists the problem of how to define the initial query compounds and which of their conformations should be used. Here, we propose a novel shape plus surface property approach using multiple local spherical harmonic (SH) functions. We also investigate the use of shape-based and shape plus property-based consensus SH queries calculated in several different ways. The utility of these approaches is compared using the 40 pharmaceutically relevant targets of the DUD database. Our results show that using a combination of SH-based properties often gives better VS performance than using simple shape-based queries. Shape-based consensus queries also perform well, but we find that explicit 3D shape-property conformations should be retained for highly flexible ligands.</div></front></TEI></HAL><ISTEX><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using Spherical Harmonic Surface Property Representations for Ligand‐Based Virtual Screening</title><author><name sortKey="Perez Ueno, Violeta I" sort="Perez Ueno, Violeta I" uniqKey="Perez Ueno V" first="Violeta I." last="Pérez-Nueno">Violeta I. Pérez-Nueno</name></author><author><name sortKey="Venkatraman, Vishwesh" sort="Venkatraman, Vishwesh" uniqKey="Venkatraman V" first="Vishwesh" last="Venkatraman">Vishwesh Venkatraman</name></author><author><name sortKey="Mavridis, Lazaros" sort="Mavridis, Lazaros" uniqKey="Mavridis L" first="Lazaros" last="Mavridis">Lazaros Mavridis</name></author><author><name sortKey="Clark, Tim" sort="Clark, Tim" uniqKey="Clark T" first="Tim" last="Clark">Tim Clark</name></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:328759D58EA3960AE5933ED4FD47E234F87B4F02</idno><date when="2011" year="2011">2011</date><idno type="doi">10.1002/minf.201000149</idno><idno type="url">https://api.istex.fr/ark:/67375/WNG-9CDQ1JF2-K/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">000B85</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000B85</idno><idno type="wicri:Area/Istex/Curation">000B78</idno><idno type="wicri:Area/Istex/Checkpoint">000510</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000510</idno><idno type="wicri:doubleKey">1868-1743:2011:Perez Ueno V:using:spherical:harmonic</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Using Spherical Harmonic Surface Property Representations for Ligand‐Based Virtual Screening</title><author><name sortKey="Perez Ueno, Violeta I" sort="Perez Ueno, Violeta I" uniqKey="Perez Ueno V" first="Violeta I." last="Pérez-Nueno">Violeta I. Pérez-Nueno</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Equipe Orpailleur, INRIA Nancy – Grand Est, LORIA, 54506 Vandoeuvre‐lès‐Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandoeuvre‐lès‐Nancy</settlement></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Allemagne</country></affiliation><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Correspondence address: Equipe Orpailleur, INRIA Nancy – Grand Est, LORIA, 54506 Vandoeuvre‐lès‐Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandoeuvre‐lès‐Nancy</settlement></placeName></affiliation></author><author><name sortKey="Venkatraman, Vishwesh" sort="Venkatraman, Vishwesh" uniqKey="Venkatraman V" first="Vishwesh" last="Venkatraman">Vishwesh Venkatraman</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Equipe Orpailleur, INRIA Nancy – Grand Est, LORIA, 54506 Vandoeuvre‐lès‐Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandoeuvre‐lès‐Nancy</settlement></placeName></affiliation></author><author><name sortKey="Mavridis, Lazaros" sort="Mavridis, Lazaros" uniqKey="Mavridis L" first="Lazaros" last="Mavridis">Lazaros Mavridis</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Equipe Orpailleur, INRIA Nancy – Grand Est, LORIA, 54506 Vandoeuvre‐lès‐Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandoeuvre‐lès‐Nancy</settlement></placeName></affiliation></author><author><name sortKey="Clark, Tim" sort="Clark, Tim" uniqKey="Clark T" first="Tim" last="Clark">Tim Clark</name><affiliation wicri:level="1"><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich‐Alexander‐Universität Erlangen‐Nürnberg, Egerlandstrasse 3, 91058 Erlangen</wicri:regionArea><placeName><settlement type="city">Erlangen</settlement><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Moyenne-Franconie</region></placeName></affiliation></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Equipe Orpailleur, INRIA Nancy – Grand Est, LORIA, 54506 Vandoeuvre‐lès‐Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandoeuvre‐lès‐Nancy</settlement></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Molecular Informatics</title><title level="j" type="sub">18th European Symposium on Quantitative Structure‐Activity Relationships (EuroQSAR 2010), September 19–24, 2010, Rhodes, Greece</title><title level="j" type="alt">MOLECULAR INFORMATICS</title><idno type="ISSN">1868-1743</idno><idno type="eISSN">1868-1751</idno><imprint><biblScope unit="vol">30</biblScope><biblScope unit="issue">2‐3</biblScope><biblScope unit="page" from="151">151</biblScope><biblScope unit="page" to="159">159</biblScope><biblScope unit="page-count">9</biblScope><publisher>WILEY‐VCH Verlag</publisher><pubPlace>Weinheim</pubPlace><date type="published" when="2011-03-14">2011-03-14</date></imprint><idno type="ISSN">1868-1743</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1868-1743</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Active ligands</term><term>Analogue bias</term><term>Binding pocket</term><term>Case study</term><term>Centre</term><term>Centre conf</term><term>Centre molecule</term><term>Chem</term><term>Chemical information</term><term>Compound level</term><term>Conf</term><term>Conformation</term><term>Conformational level</term><term>Consensus</term><term>Consensus cluster</term><term>Consensus conf</term><term>Consensus conformation</term><term>Consensus molecule</term><term>Consensus properties</term><term>Consensus shape</term><term>Consensus shape approach</term><term>Conventional queries</term><term>Crystal query</term><term>Crystal structure</term><term>Crystallographic query</term><term>Database</term><term>Different queries</term><term>Different ways</term><term>Difficult targets</term><term>Early performance</term><term>Early recognition</term><term>Early recognition performance</term><term>Enrichment factor</term><term>Expansion order</term><term>First stage</term><term>Flexible ligands</term><term>Full paper violeta</term><term>Genetic algorithm</term><term>Gmbh</term><term>Initial query compounds</term><term>Kgaa</term><term>Large number</term><term>Ligand</term><term>Local properties</term><term>Local surface properties</term><term>Molecule</term><term>Multiple ligands</term><term>Overall performance</term><term>Parafit</term><term>Parafit_bound parafit_rcm parafit_cm</term><term>Property representations</term><term>Query</term><term>Query conformation</term><term>Query conformations</term><term>Query optimization</term><term>Real centre molecule</term><term>Relative success</term><term>Results show</term><term>Rocs query</term><term>Rotatable bonds</term><term>Screening</term><term>Screening performance</term><term>Second stage</term><term>Surface properties</term><term>Surface property representations</term><term>Surface shape</term><term>Surface shapes</term><term>Verlag</term><term>Verlag gmbh</term><term>Virtual screening</term><term>Weighted properties</term><term>Weinheim</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ligand‐based virtual screening (VS) techniques have become well established in the drug discovery process. However, despite their relative success, there still exists the problem of how to define the initial query compounds and which of their conformations should be used. Here, we propose a novel shape plus surface property approach using multiple local spherical harmonic (SH) functions. We also investigate the use of shape‐based and shape plus property‐based consensus SH queries calculated in several different ways. The utility of these approaches is compared using the 40 pharmaceutically relevant targets of the DUD database. Our results show that using a combination of SH‐based properties often gives better VS performance than using simple shape‐based queries. Shape‐based consensus queries also perform well, but we find that explicit 3D shape‐property conformations should be retained for highly flexible ligands.</div></front></TEI></ISTEX></double></record>Pour manipuler ce document sous Unix (Dilib)
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