PubChem3D: a new resource for scientists
Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse c...
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| Published in | Journal of cheminformatics Vol. 3; no. 1; p. 32 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Cham
Springer International Publishing
20.09.2011
BioMed Central Ltd Springer Nature B.V BioMed Central BMC |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1758-2946 1758-2946 |
| DOI | 10.1186/1758-2946-3-32 |
Cover
| Abstract | Background
PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis.
Description
PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.
A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity.
Conclusions
The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. |
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| AbstractList | PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. Abstract Background: PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. Description: PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data. A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. Conclusions: The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. Description PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data. A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. Conclusions The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. Description PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data. A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. Conclusions The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis.BACKGROUNDPubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis.PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity.DESCRIPTIONPubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity.The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem.CONCLUSIONSThe addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. |
| ArticleNumber | 32 |
| Audience | Academic |
| Author | Kim, Sunghwan Zhang, Jian Bryant, Stephen H Simonyan, Vahan Chen, Jie Han, Lianyi He, Siqian Sun, Yan Shi, Wenyao Wang, Jiyao Thiessen, Paul A Yu, Bo Bolton, Evan E |
| AuthorAffiliation | 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA |
| AuthorAffiliation_xml | – name: 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA |
| Author_xml | – sequence: 1 givenname: Evan E surname: Bolton fullname: Bolton, Evan E email: bolton@ncbi.nlm.nih.gov organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 2 givenname: Jie surname: Chen fullname: Chen, Jie organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 3 givenname: Sunghwan surname: Kim fullname: Kim, Sunghwan organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 4 givenname: Lianyi surname: Han fullname: Han, Lianyi organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 5 givenname: Siqian surname: He fullname: He, Siqian organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 6 givenname: Wenyao surname: Shi fullname: Shi, Wenyao organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 7 givenname: Vahan surname: Simonyan fullname: Simonyan, Vahan organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 8 givenname: Yan surname: Sun fullname: Sun, Yan organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 9 givenname: Paul A surname: Thiessen fullname: Thiessen, Paul A organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 10 givenname: Jiyao surname: Wang fullname: Wang, Jiyao organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 11 givenname: Bo surname: Yu fullname: Yu, Bo organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 12 givenname: Jian surname: Zhang fullname: Zhang, Jian organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health – sequence: 13 givenname: Stephen H surname: Bryant fullname: Bryant, Stephen H organization: National Center for Biotechnology Information, National Library of Medicine, Department of Health and Human Services, National Institutes of Health |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/21933373$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1186/1758-2946-3-25 10.1186/1752-153X-1-12 10.1186/1758-2946-3-4 10.1186/1758-2946-3-9 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P 10.1023/A:1015930826903 10.1126/science.257.5073.1078 10.1016/j.tibtech.2009.02.003 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X 10.1517/17460441.2010.513711 10.1007/BF00134183 10.1186/1758-2946-3-26 10.1021/ci100031x 10.1093/nar/gkp965 10.1038/nrmicro2349 10.2174/1381612053382106 10.1093/nar/gkl320 10.1021/ci060042s 10.1111/j.1747-0285.2009.00899.x 10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W 10.1021/ci00010a010 10.1021/ci000100o 10.1021/j100011a016 10.1021/jm1013693 10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K 10.2174/156802609789207127 10.1186/1758-2946-3-13 10.1093/nar/gkp456 10.1007/978-94-017-1120-3_5 10.1093/nar/gkq1172 10.1021/jm900818s |
| ContentType | Journal Article |
| Copyright | Bolton et al; licensee Chemistry Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. COPYRIGHT 2011 BioMed Central Ltd. 2011 Bolton et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copyright ©2011 Bolton et al; licensee Chemistry Central Ltd. 2011 Bolton et al; licensee Chemistry Central Ltd. |
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| DOI | 10.1186/1758-2946-3-32 |
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| References | Andricopulo, Salum, Abraham (CR20) 2009; 9 Halgren (CR25) 1996; 17 Bolton, Kim, Bryant (CR8) 2011; 3 Bolton, Wang, Thiessen, Bryant, Ralph, David (CR1) 2008 Mansfield, Covell, Jernigan (CR42) 2002; 42 CR38 CR15 Kim, Bolton, Bryant (CR9) 2011; 3 CR14 van Montfort, Workman (CR21) 2009; 27 CR36 CR31 CR30 Bolton, Kim, Bryant (CR6) 2011; 3 Meanwell (CR16) 2011; 54 Sadowski, Bostrom (CR34) 2006; 46 Sayers, Barrett, Benson, Bolton, Bryant, Canese, Chetvernin, Church, DiCuccio, Federhen (CR4) 2011; 39 Hull, Wolstencroft, Stevens, Goble, Pocock, Li, Oinn (CR44) 2006; 34 Lajiness, Johnson, Maggiora (CR40) 1989; 291 Chan, Brown, Hedrick, Rascon, Millan, Sergienko, Roth, Reddy, Dad, Chung (CR46) 2010 Sun, Scott (CR22) 2010; 75 Fontaine, Bolton, Borodina, Bryant (CR41) 2007; 1 Wang, Xiao, Suzek, Zhang, Wang, Bryant (CR2) 2009; 37 Halgren (CR24) 1996; 17 CR5 Mohan, Gibbs, Cummings, Jaeger, DesJarlais (CR18) 2005; 11 Grant, Gallardo, Pickup (CR12) 1996; 17 CR29 Grant, Pickup (CR11) 1995; 99 CR28 Mills, Dean (CR37) 1996; 10 CR27 Bostrom (CR35) 2001; 15 CR47 Wang, Bolton, Dracheva, Karapetyan, Shoemaker, Suzek, Wang, Xiao, Zhang, Bryant (CR3) 2010; 38 Grant, Pickup, van Gunsteren, Weiner, Wilkinson (CR13) 1997 CR45 Nicholls, McGaughey, Sheridan, Good, Warren, Mathieu, Muchmore, Brown, Grant, Haigh (CR17) 2010; 53 CR43 Hawkins, Skillman, Warren, Ellingson, Stahl (CR33) 2010; 50 Barnard, Downs (CR39) 1992; 32 Simmons, Chopra, Fishwick (CR19) 2010; 8 Halgren (CR26) 1999; 20 Musafia, Senderowitz (CR32) 2010; 5 Kim, Bolton, Bryant (CR10) 2011; 3 Kuntz (CR23) 1992; 257 Bolton, Kim, Bryant (CR7) 2011; 3 H Sun (231_CR22) 2010; 75 B Musafia (231_CR32) 2010; 5 TA Halgren (231_CR25) 1996; 17 EE Bolton (231_CR8) 2011; 3 X Chan (231_CR46) 2010 D Hull (231_CR44) 2006; 34 231_CR30 231_CR31 A Nicholls (231_CR17) 2010; 53 KJ Simmons (231_CR19) 2010; 8 YL Wang (231_CR3) 2010; 38 JA Grant (231_CR12) 1996; 17 231_CR47 231_CR27 231_CR28 231_CR29 EE Bolton (231_CR6) 2011; 3 NA Meanwell (231_CR16) 2011; 54 EE Bolton (231_CR1) 2008 JM Barnard (231_CR39) 1992; 32 J Sadowski (231_CR34) 2006; 46 TA Halgren (231_CR24) 1996; 17 JA Grant (231_CR11) 1995; 99 EE Bolton (231_CR7) 2011; 3 JEJ Mills (231_CR37) 1996; 10 231_CR5 JA Grant (231_CR13) 1997 V Mohan (231_CR18) 2005; 11 RLM van Montfort (231_CR21) 2009; 27 231_CR43 231_CR45 AD Andricopulo (231_CR20) 2009; 9 231_CR14 231_CR36 231_CR15 YL Wang (231_CR2) 2009; 37 PCD Hawkins (231_CR33) 2010; 50 231_CR38 MS Lajiness (231_CR40) 1989; 291 ML Mansfield (231_CR42) 2002; 42 TA Halgren (231_CR26) 1999; 20 S Kim (231_CR10) 2011; 3 EW Sayers (231_CR4) 2011; 39 F Fontaine (231_CR41) 2007; 1 J Bostrom (231_CR35) 2001; 15 S Kim (231_CR9) 2011; 3 ID Kuntz (231_CR23) 1992; 257 20551974 - Nat Rev Microbiol. 2010 Jul;8(7):501-10 12160095 - J Comput Aided Mol Des. 2001 Dec;15(12):1137-52 21418625 - J Cheminform. 2011 Mar 21;3:9 19933261 - Nucleic Acids Res. 2010 Jan;38(Database issue):D255-66 19754394 - Curr Top Med Chem. 2009;9(9):771-90 17880744 - Chem Cent J. 2007 Jun 06;1:12 1509259 - Science. 1992 Aug 21;257(5073):1078-82 20235588 - J Chem Inf Model. 2010 Apr 26;50(4):572-84 11911695 - J Chem Inf Comput Sci. 2002 Mar-Apr;42(2):259-73 21272340 - J Cheminform. 2011 Jan 27;3(1):4 21413808 - J Med Chem. 2011 Apr 28;54(8):2529-91 19339067 - Trends Biotechnol. 2009 May;27(5):315-28 22823989 - Expert Opin Drug Discov. 2010 Oct;5(10):943-59 21097890 - Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51 21554721 - J Cheminform. 2011 May 09;3:13 21774809 - J Cheminform. 2011 Jul 20;3:25 19498078 - Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33 15723628 - Curr Pharm Des. 2005;11(3):323-33 2726841 - Prog Clin Biol Res. 1989;291:173-6 20158188 - J Med Chem. 2010 May 27;53(10):3862-86 21781288 - J Cheminform. 2011 Jul 22;3(1):26 17125173 - J Chem Inf Model. 2006 Nov-Dec;46(6):2305-9 19878193 - Chem Biol Drug Des. 2010 Jan;75(1):3-17 9007693 - J Comput Aided Mol Des. 1996 Dec;10(6):607-22 16845108 - Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32 |
| References_xml | – ident: CR45 – volume: 3 start-page: 25 year: 2011 ident: CR9 article-title: PubChem3D: shape compatibility filtering using molecular shape quadrupoles publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-25 – volume: 1 start-page: 12 year: 2007 ident: CR41 article-title: Fast 3D shape screening of large chemical databases through alignment-recycling publication-title: Chem Cent J doi: 10.1186/1752-153X-1-12 – ident: CR43 – volume: 3 start-page: 4 year: 2011 ident: CR6 article-title: PubChem3D: conformer generation publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-4 – volume: 3 start-page: 9 year: 2011 ident: CR7 article-title: PubChem3D: diversity of shape publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-9 – ident: CR47 – volume: 17 start-page: 490 year: 1996 end-page: 519 ident: CR24 article-title: Merck molecular force field. 1. Basis, form, scope, parameterization, and performance of MMFF94 publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P – volume: 15 start-page: 1137 year: 2001 end-page: 1152 ident: CR35 article-title: Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools publication-title: J Comput Aided Mol Des doi: 10.1023/A:1015930826903 – ident: CR14 – ident: CR30 – volume: 257 start-page: 1078 year: 1992 end-page: 1082 ident: CR23 article-title: Structure-based strategies for drug design and discovery publication-title: Science doi: 10.1126/science.257.5073.1078 – year: 2010 ident: CR46 article-title: HTS identification of compounds activating TNAP at an intermediate concentration of phosphate acceptor detected in luminescent assay publication-title: Probe Reports from the NIH Molecular Libraries Program – ident: CR29 – volume: 27 start-page: 315 year: 2009 end-page: 328 ident: CR21 article-title: Structure-based design of molecular cancer therapeutics publication-title: Trends Biotechnol doi: 10.1016/j.tibtech.2009.02.003 – volume: 20 start-page: 720 year: 1999 end-page: 729 ident: CR26 article-title: MMFF VI. MMFF94s option for energy minimization studies publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X – volume: 5 start-page: 943 year: 2010 end-page: 959 ident: CR32 article-title: Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design publication-title: Expert Opin Drug Discov doi: 10.1517/17460441.2010.513711 – volume: 10 start-page: 607 year: 1996 end-page: 622 ident: CR37 article-title: Three-dimensional hydrogen-bond geometry and probability information from a crystal survey publication-title: J Comput Aided Mol Des doi: 10.1007/BF00134183 – ident: CR27 – volume: 3 start-page: 26 year: 2011 ident: CR10 article-title: PubChem3D: biologically relevant 3-D similarity publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-26 – volume: 50 start-page: 572 year: 2010 end-page: 584 ident: CR33 article-title: Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database publication-title: J Chem Inf Model doi: 10.1021/ci100031x – volume: 38 start-page: D255 year: 2010 end-page: D266 ident: CR3 article-title: An overview of the PubChem BioAssay resource publication-title: Nucleic Acids Res doi: 10.1093/nar/gkp965 – volume: 8 start-page: 501 year: 2010 end-page: 510 ident: CR19 article-title: Structure-based discovery of antibacterial drugs publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2349 – volume: 11 start-page: 323 year: 2005 end-page: 333 ident: CR18 article-title: Docking: successes and challenges publication-title: Curr Pharm Design doi: 10.2174/1381612053382106 – volume: 291 start-page: 173 year: 1989 end-page: 176 ident: CR40 article-title: Implementing drug screening programs using molecular similarity methods publication-title: Prog Clin Biol Res – volume: 34 start-page: W729 year: 2006 end-page: W732 ident: CR44 article-title: Taverna: a tool for building and running workflows of services publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl320 – volume: 46 start-page: 2305 year: 2006 end-page: 2309 ident: CR34 article-title: MIMUMBA revisited: Torsion angle rules for conformer generation derived from X-ray structures publication-title: J Chem Inf Model doi: 10.1021/ci060042s – ident: CR15 – volume: 75 start-page: 3 year: 2010 end-page: 17 ident: CR22 article-title: Structure-based drug metabolism predictions for drug design publication-title: Chem Biol Drug Des doi: 10.1111/j.1747-0285.2009.00899.x – volume: 17 start-page: 520 year: 1996 end-page: 552 ident: CR25 article-title: Merck molecular force field. 2. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W – ident: CR38 – volume: 32 start-page: 644 year: 1992 end-page: 649 ident: CR39 article-title: Clustering of chemical structures on the basis of two-dimensional similarity measures publication-title: J Chem Inf Comput Sci doi: 10.1021/ci00010a010 – volume: 42 start-page: 259 year: 2002 end-page: 273 ident: CR42 article-title: A new class of molecular shape descriptors. 1. Theory and properties publication-title: J Chem Inf Comput Sci doi: 10.1021/ci000100o – ident: CR31 – volume: 99 start-page: 3503 year: 1995 end-page: 3510 ident: CR11 article-title: A Gaussian description of molecular shape publication-title: J Phys Chem doi: 10.1021/j100011a016 – volume: 54 start-page: 2529 year: 2011 end-page: 2591 ident: CR16 article-title: Synopsis of some recent tactical application of bioisosteres in drug design publication-title: J Med Chem doi: 10.1021/jm1013693 – start-page: 217 year: 2008 end-page: 241 ident: CR1 article-title: PubChem: integrated platform of small molecules and biological activities publication-title: Annual Reports in Computational Chemistry – volume: 17 start-page: 1653 year: 1996 end-page: 1666 ident: CR12 article-title: A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K – volume: 9 start-page: 771 year: 2009 end-page: 790 ident: CR20 article-title: Structure-based drug design strategies in medicinal chemistry publication-title: Curr Top Med Chem doi: 10.2174/156802609789207127 – ident: CR36 – ident: CR5 – volume: 3 start-page: 13 year: 2011 ident: CR8 article-title: PubChem3D: similar conformers publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-13 – volume: 37 start-page: W623 year: 2009 end-page: W633 ident: CR2 article-title: PubChem: a public information system for analyzing bioactivities of small molecules publication-title: Nucleic Acids Res doi: 10.1093/nar/gkp456 – start-page: 150 year: 1997 end-page: 176 ident: CR13 article-title: Gaussian shape methods publication-title: Computer Simulation of Biomolecular Systems doi: 10.1007/978-94-017-1120-3_5 – volume: 39 start-page: D38 year: 2011 end-page: D51 ident: CR4 article-title: Database resources of the National Center for Biotechnology Information publication-title: Nucleic Acids Res doi: 10.1093/nar/gkq1172 – ident: CR28 – volume: 53 start-page: 3862 year: 2010 end-page: 3886 ident: CR17 article-title: Molecular shape and medicinal chemistry: a perspective publication-title: J Med Chem doi: 10.1021/jm900818s – ident: 231_CR29 – ident: 231_CR27 – volume: 50 start-page: 572 year: 2010 ident: 231_CR33 publication-title: J Chem Inf Model doi: 10.1021/ci100031x – volume: 15 start-page: 1137 year: 2001 ident: 231_CR35 publication-title: J Comput Aided Mol Des doi: 10.1023/A:1015930826903 – ident: 231_CR5 – volume: 38 start-page: D255 year: 2010 ident: 231_CR3 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkp965 – ident: 231_CR31 – start-page: 217 volume-title: Annual Reports in Computational Chemistry year: 2008 ident: 231_CR1 – volume: 9 start-page: 771 year: 2009 ident: 231_CR20 publication-title: Curr Top Med Chem doi: 10.2174/156802609789207127 – volume: 3 start-page: 4 year: 2011 ident: 231_CR6 publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-4 – volume: 17 start-page: 1653 year: 1996 ident: 231_CR12 publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K – volume: 99 start-page: 3503 year: 1995 ident: 231_CR11 publication-title: J Phys Chem doi: 10.1021/j100011a016 – volume: 27 start-page: 315 year: 2009 ident: 231_CR21 publication-title: Trends Biotechnol doi: 10.1016/j.tibtech.2009.02.003 – volume: 75 start-page: 3 year: 2010 ident: 231_CR22 publication-title: Chem Biol Drug Des doi: 10.1111/j.1747-0285.2009.00899.x – ident: 231_CR14 – volume: 3 start-page: 9 year: 2011 ident: 231_CR7 publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-9 – volume: 291 start-page: 173 year: 1989 ident: 231_CR40 publication-title: Prog Clin Biol Res – start-page: 150 volume-title: Computer Simulation of Biomolecular Systems year: 1997 ident: 231_CR13 doi: 10.1007/978-94-017-1120-3_5 – volume: 54 start-page: 2529 year: 2011 ident: 231_CR16 publication-title: J Med Chem doi: 10.1021/jm1013693 – volume: 39 start-page: D38 year: 2011 ident: 231_CR4 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkq1172 – volume: 17 start-page: 520 year: 1996 ident: 231_CR25 publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W – volume: 46 start-page: 2305 year: 2006 ident: 231_CR34 publication-title: J Chem Inf Model doi: 10.1021/ci060042s – volume: 10 start-page: 607 year: 1996 ident: 231_CR37 publication-title: J Comput Aided Mol Des doi: 10.1007/BF00134183 – ident: 231_CR28 – volume: 257 start-page: 1078 year: 1992 ident: 231_CR23 publication-title: Science doi: 10.1126/science.257.5073.1078 – ident: 231_CR30 – volume: 53 start-page: 3862 year: 2010 ident: 231_CR17 publication-title: J Med Chem doi: 10.1021/jm900818s – volume: 8 start-page: 501 year: 2010 ident: 231_CR19 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2349 – volume: 17 start-page: 490 year: 1996 ident: 231_CR24 publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P – volume: 3 start-page: 13 year: 2011 ident: 231_CR8 publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-13 – volume-title: Probe Reports from the NIH Molecular Libraries Program year: 2010 ident: 231_CR46 – ident: 231_CR47 – ident: 231_CR45 – volume: 3 start-page: 25 year: 2011 ident: 231_CR9 publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-25 – volume: 32 start-page: 644 year: 1992 ident: 231_CR39 publication-title: J Chem Inf Comput Sci doi: 10.1021/ci00010a010 – ident: 231_CR15 – ident: 231_CR43 – volume: 34 start-page: W729 year: 2006 ident: 231_CR44 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl320 – volume: 1 start-page: 12 year: 2007 ident: 231_CR41 publication-title: Chem Cent J doi: 10.1186/1752-153X-1-12 – volume: 3 start-page: 26 year: 2011 ident: 231_CR10 publication-title: J Cheminformatics doi: 10.1186/1758-2946-3-26 – volume: 5 start-page: 943 year: 2010 ident: 231_CR32 publication-title: Expert Opin Drug Discov doi: 10.1517/17460441.2010.513711 – volume: 20 start-page: 720 year: 1999 ident: 231_CR26 publication-title: J Comput Chem doi: 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X – ident: 231_CR36 – volume: 11 start-page: 323 year: 2005 ident: 231_CR18 publication-title: Curr Pharm Design doi: 10.2174/1381612053382106 – volume: 42 start-page: 259 year: 2002 ident: 231_CR42 publication-title: J Chem Inf Comput Sci doi: 10.1021/ci000100o – ident: 231_CR38 – volume: 37 start-page: W623 year: 2009 ident: 231_CR2 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkp456 – reference: 21554721 - J Cheminform. 2011 May 09;3:13 – reference: 19339067 - Trends Biotechnol. 2009 May;27(5):315-28 – reference: 1509259 - Science. 1992 Aug 21;257(5073):1078-82 – reference: 19754394 - Curr Top Med Chem. 2009;9(9):771-90 – reference: 19878193 - Chem Biol Drug Des. 2010 Jan;75(1):3-17 – reference: 21413808 - J Med Chem. 2011 Apr 28;54(8):2529-91 – reference: 21781288 - J Cheminform. 2011 Jul 22;3(1):26 – reference: 20235588 - J Chem Inf Model. 2010 Apr 26;50(4):572-84 – reference: 15723628 - Curr Pharm Des. 2005;11(3):323-33 – reference: 21774809 - J Cheminform. 2011 Jul 20;3:25 – reference: 20158188 - J Med Chem. 2010 May 27;53(10):3862-86 – reference: 17125173 - J Chem Inf Model. 2006 Nov-Dec;46(6):2305-9 – reference: 19933261 - Nucleic Acids Res. 2010 Jan;38(Database issue):D255-66 – reference: 17880744 - Chem Cent J. 2007 Jun 06;1:12 – reference: 2726841 - Prog Clin Biol Res. 1989;291:173-6 – reference: 21272340 - J Cheminform. 2011 Jan 27;3(1):4 – reference: 11911695 - J Chem Inf Comput Sci. 2002 Mar-Apr;42(2):259-73 – reference: 20551974 - Nat Rev Microbiol. 2010 Jul;8(7):501-10 – reference: 19498078 - Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33 – reference: 16845108 - Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32 – reference: 22823989 - Expert Opin Drug Discov. 2010 Oct;5(10):943-59 – reference: 21097890 - Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51 – reference: 12160095 - J Comput Aided Mol Des. 2001 Dec;15(12):1137-52 – reference: 9007693 - J Comput Aided Mol Des. 1996 Dec;10(6):607-22 – reference: 21418625 - J Cheminform. 2011 Mar 21;3:9 |
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| Snippet | Background
PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval,... PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization,... Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval,... Abstract Background: PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search,... Abstract Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search,... |
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| SubjectTerms | Analysis Archives & records Chemistry Chemistry and Materials Science Computational Biology/Bioinformatics Computer Applications in Chemistry Data mining Documentation and Information in Chemistry PubChem3D Scientists Software Theoretical and Computational Chemistry |
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| Title | PubChem3D: a new resource for scientists |
| URI | https://link.springer.com/article/10.1186/1758-2946-3-32 https://www.ncbi.nlm.nih.gov/pubmed/21933373 https://www.proquest.com/docview/905755854 https://www.proquest.com/docview/906154158 https://pubmed.ncbi.nlm.nih.gov/PMC3269824 https://doaj.org/article/d7187b96a1b64e3b842975826f3023fe |
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