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A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. Sampling can be tailored to a specific structural domain (e.g., peptides) by extracting torsional profiles from specific datasets and subsequently applying...
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Published in: | Journal of computer-aided molecular design 2008-09, Vol.22 (9), p.681-691 |
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container_title | Journal of computer-aided molecular design |
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creator | Dorfman, Roman J. Smith, Karl M. Masek, Brian B. Clark, Robert D. |
description | This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. Sampling can be tailored to a specific structural domain (e.g., peptides) by extracting torsional profiles from specific datasets and subsequently applying them to target molecules outside the reference set. The programs that handle creation of the knowledge-based torsional profiles and conformer generation per se are separate and so can be used independently or sequentially, depending on the task at hand. The conformational ensembles produced are contrasted with those generated using local minimization approaches. They are also quantitatively compared with a broader range of techniques in terms of speed and the ability to reproduce bound ligand conformations found in complexes with proteins. |
doi_str_mv | 10.1007/s10822-007-9156-5 |
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They are also quantitatively compared with a broader range of techniques in terms of speed and the ability to reproduce bound ligand conformations found in complexes with proteins.</description><identifier>ISSN: 0920-654X</identifier><identifier>EISSN: 1573-4951</identifier><identifier>DOI: 10.1007/s10822-007-9156-5</identifier><identifier>PMID: 18058240</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Biophysics ; Chemistry ; Chemistry and Materials Science ; Computer Applications in Chemistry ; Endothelin-1 - antagonists & inhibitors ; Endothelin-1 - metabolism ; Histology ; Knowledge Bases ; Ligands ; Models, Molecular ; Molecular biology ; Molecular Conformation ; Morphology ; Pharmaceutical Preparations - chemistry ; Pharmacology ; Physical Chemistry ; Proteins</subject><ispartof>Journal of computer-aided molecular design, 2008-09, Vol.22 (9), p.681-691</ispartof><rights>Springer Science+Business Media B.V. 2007</rights><rights>Springer Science+Business Media B.V. 2008</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c369t-a93ecc926f53b599f84e2fc082686f975f257c320a0e07e9d231554a332631353</citedby><cites>FETCH-LOGICAL-c369t-a93ecc926f53b599f84e2fc082686f975f257c320a0e07e9d231554a332631353</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18058240$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dorfman, Roman J.</creatorcontrib><creatorcontrib>Smith, Karl M.</creatorcontrib><creatorcontrib>Masek, Brian B.</creatorcontrib><creatorcontrib>Clark, Robert D.</creatorcontrib><title>A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers</title><title>Journal of computer-aided molecular design</title><addtitle>J Comput Aided Mol Des</addtitle><addtitle>J Comput Aided Mol Des</addtitle><description>This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. 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antagonists & inhibitors</topic><topic>Endothelin-1 - metabolism</topic><topic>Histology</topic><topic>Knowledge Bases</topic><topic>Ligands</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Molecular Conformation</topic><topic>Morphology</topic><topic>Pharmaceutical Preparations - chemistry</topic><topic>Pharmacology</topic><topic>Physical Chemistry</topic><topic>Proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dorfman, Roman J.</creatorcontrib><creatorcontrib>Smith, Karl M.</creatorcontrib><creatorcontrib>Masek, Brian B.</creatorcontrib><creatorcontrib>Clark, Robert D.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Computer and Information Systems Abstracts</collection><collection>ProQuest Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology 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)</collection><collection>ProQuest Central</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Materials Science Database</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>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Science Journals</collection><collection>ProQuest Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</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>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of computer-aided molecular design</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dorfman, Roman J.</au><au>Smith, Karl M.</au><au>Masek, Brian B.</au><au>Clark, Robert D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers</atitle><jtitle>Journal of computer-aided molecular design</jtitle><stitle>J Comput Aided Mol Des</stitle><addtitle>J Comput Aided Mol Des</addtitle><date>2008-09-01</date><risdate>2008</risdate><volume>22</volume><issue>9</issue><spage>681</spage><epage>691</epage><pages>681-691</pages><issn>0920-654X</issn><eissn>1573-4951</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. 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subjects | Animal Anatomy Biophysics Chemistry Chemistry and Materials Science Computer Applications in Chemistry Endothelin-1 - antagonists & inhibitors Endothelin-1 - metabolism Histology Knowledge Bases Ligands Models, Molecular Molecular biology Molecular Conformation Morphology Pharmaceutical Preparations - chemistry Pharmacology Physical Chemistry Proteins |
title | A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers |
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