LiGen: A High Performance Workflow for Chemistry Driven de Novo Design
Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or...
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| Veröffentlicht in: | Journal of chemical information and modeling 2013-06, Vol.53 (6), p.1518-1527 |
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| container_title | Journal of chemical information and modeling |
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| creator | Beccari, Andrea R Cavazzoni, Carlo Beato, Claudia Costantino, Gabriele |
| description | Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented. |
| doi_str_mv | 10.1021/ci400078g |
| format | Article |
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Chem. Inf. Model</addtitle><description>Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented.</description><subject>Applied sciences</subject><subject>Biological and medical sciences</subject><subject>Chemicals</subject><subject>Computer science; control theory; systems</subject><subject>Drug Design</subject><subject>Exact sciences and technology</subject><subject>General pharmacology</subject><subject>Identification</subject><subject>Information systems. Data bases</subject><subject>Ligands</subject><subject>Mapping</subject><subject>Medical sciences</subject><subject>Memory organisation. Data processing</subject><subject>Molecular Docking Simulation</subject><subject>Pharmaceutical technology. Pharmaceutical industry</subject><subject>Pharmacology. 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Drug treatments</topic><topic>Software</topic><topic>Workflow</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Beccari, Andrea R</creatorcontrib><creatorcontrib>Cavazzoni, Carlo</creatorcontrib><creatorcontrib>Beato, Claudia</creatorcontrib><creatorcontrib>Costantino, Gabriele</creatorcontrib><collection>Pascal-Francis</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>Beccari, Andrea R</au><au>Cavazzoni, Carlo</au><au>Beato, Claudia</au><au>Costantino, Gabriele</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LiGen: A High Performance Workflow for Chemistry Driven de Novo Design</atitle><jtitle>Journal of chemical information and modeling</jtitle><addtitle>J. Chem. Inf. Model</addtitle><date>2013-06-24</date><risdate>2013</risdate><volume>53</volume><issue>6</issue><spage>1518</spage><epage>1527</epage><pages>1518-1527</pages><issn>1549-9596</issn><eissn>1549-960X</eissn><abstract>Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. 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| identifier | ISSN: 1549-9596 |
| ispartof | Journal of chemical information and modeling, 2013-06, Vol.53 (6), p.1518-1527 |
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| source | MEDLINE; American Chemical Society Journals |
| subjects | Applied sciences Biological and medical sciences Chemicals Computer science control theory systems Drug Design Exact sciences and technology General pharmacology Identification Information systems. Data bases Ligands Mapping Medical sciences Memory organisation. Data processing Molecular Docking Simulation Pharmaceutical technology. Pharmaceutical industry Pharmacology. Drug treatments Software Workflow |
| title | LiGen: A High Performance Workflow for Chemistry Driven de Novo Design |
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