Literature DB >> 20970519

PubChem as a public resource for drug discovery.

Qingliang Li1, Tiejun Cheng, Yanli Wang, Stephen H Bryant.   

Abstract

PubChem is a public repository of small molecules and their biological properties. Currently, it contains more than 25 million unique chemical structures and 90 million bioactivity outcomes associated with several thousand macromolecular targets. To address the potential utility of this public resource for drug discovery, we systematically summarized the protein targets in PubChem by function, 3D structure and biological pathway. Moreover, we analyzed the potency, selectivity and promiscuity of the bioactive compounds identified for these biological targets, including the chemical probes generated by the NIH Molecular Libraries Program. As a public resource, PubChem lowers the barrier for researchers to advance the development of chemical tools for modulating biological processes and drug candidates for disease treatments. Published by Elsevier Ltd.

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Year:  2010        PMID: 20970519      PMCID: PMC3010383          DOI: 10.1016/j.drudis.2010.10.003

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  31 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The druggable genome: an update.

Authors:  Andreas P Russ; Stefan Lampel
Journal:  Drug Discov Today       Date:  2005-12       Impact factor: 7.851

Review 3.  How many drug targets are there?

Authors:  John P Overington; Bissan Al-Lazikani; Andrew L Hopkins
Journal:  Nat Rev Drug Discov       Date:  2006-12       Impact factor: 84.694

4.  PubChem as a source of polypharmacology.

Authors:  Bin Chen; David Wild; Rajarshi Guha
Journal:  J Chem Inf Model       Date:  2009-09       Impact factor: 4.956

Review 5.  Novel trends in high-throughput screening.

Authors:  Lorenz M Mayr; Dejan Bojanic
Journal:  Curr Opin Pharmacol       Date:  2009-09-21       Impact factor: 5.547

6.  Drug-target network.

Authors:  Muhammed A Yildirim; Kwang-Il Goh; Michael E Cusick; Albert-László Barabási; Marc Vidal
Journal:  Nat Biotechnol       Date:  2007-10       Impact factor: 54.908

7.  The art of the chemical probe.

Authors:  Stephen V Frye
Journal:  Nat Chem Biol       Date:  2010-03       Impact factor: 15.040

8.  From genomics to chemical genomics: new developments in KEGG.

Authors:  Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

9.  PubChem: a public information system for analyzing bioactivities of small molecules.

Authors:  Yanli Wang; Jewen Xiao; Tugba O Suzek; Jian Zhang; Jiyao Wang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2009-06-04       Impact factor: 16.971

10.  An overview of the PubChem BioAssay resource.

Authors:  Yanli Wang; Evan Bolton; Svetlana Dracheva; Karen Karapetyan; Benjamin A Shoemaker; Tugba O Suzek; Jiyao Wang; Jewen Xiao; Jian Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2009-11-19       Impact factor: 16.971

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  102 in total

1.  PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem.

Authors:  Stephanie A Canny; Yasel Cruz; Mark R Southern; Patrick R Griffin
Journal:  Bioinformatics       Date:  2011-11-13       Impact factor: 6.937

2.  Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Authors:  Robin Haw; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Journal:  Proteomics       Date:  2011-09       Impact factor: 3.984

3.  Extraction and validation of substructure profiles for enriching compound libraries.

Authors:  Wee Kiang Yeo; Mei Lin Go; Shahul Nilar
Journal:  J Comput Aided Mol Des       Date:  2012-09-16       Impact factor: 3.686

4.  Discovery of Small Molecule Kappa Opioid Receptor Agonist and Antagonist Chemotypes through a HTS and Hit Refinement Strategy.

Authors:  Kevin J Frankowski; Michael P Hedrick; Palak Gosalia; Kelin Li; Shenghua Shi; David Whipple; Partha Ghosh; Thomas E Prisinzano; Frank J Schoenen; Ying Su; S Vasile; Eduard Sergienko; Wilson Gray; Santosh Hariharan; Loribelle Milan; Susanne Heynen-Genel; Arianna Mangravita-Novo; Michael Vicchiarelli; Layton H Smith; John M Streicher; Marc G Caron; Lawrence S Barak; Laura M Bohn; Thomas D Y Chung; Jeffrey Aubé
Journal:  ACS Chem Neurosci       Date:  2012-01-20       Impact factor: 4.418

5.  Public domain databases for medicinal chemistry.

Authors:  George Nicola; Tiqing Liu; Michael K Gilson
Journal:  J Med Chem       Date:  2012-07-11       Impact factor: 7.446

6.  Novel multifunctional pharmacology of lobinaline, the major alkaloid from Lobelia cardinalis.

Authors:  Dustin P Brown; Dennis T Rogers; Francois Pomerleau; Kirin B Siripurapu; Manish Kulshrestha; Greg A Gerhardt; John M Littleton
Journal:  Fitoterapia       Date:  2016-04-20       Impact factor: 2.882

Review 7.  Integrated Genomic Medicine: A Paradigm for Rare Diseases and Beyond.

Authors:  N J Schork; K Nazor
Journal:  Adv Genet       Date:  2017-07-25       Impact factor: 1.944

8.  Kinome-wide activity modeling from diverse public high-quality data sets.

Authors:  Stephan C Schürer; Steven M Muskal
Journal:  J Chem Inf Model       Date:  2013-01-09       Impact factor: 4.956

9.  Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita.

Authors:  Jitendra Maharana; Banikalyan Swain; Bikash R Sahoo; Manas R Dikhit; Madhubanti Basu; Abhijit S Mahapatra; Pallipuram Jayasankar; Mrinal Samanta
Journal:  Fish Physiol Biochem       Date:  2012-12-20       Impact factor: 2.794

10.  Challenges in secondary analysis of high throughput screening data.

Authors:  Aurora S Blucher; Shannon K McWeeney
Journal:  Pac Symp Biocomput       Date:  2014
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