Literature DB >> 20889496

Chembench: a cheminformatics workbench.

Theo Walker1, Christopher M Grulke, Diane Pozefsky, Alexander Tropsha.   

Abstract

MOTIVATION: Advances in the field of cheminformatics have been hindered by a lack of freely available tools. We have created Chembench, a publicly available cheminformatics portal for analyzing experimental chemical structure-activity data. Chembench provides a broad range of tools for data visualization and embeds a rigorous workflow for creating and validating predictive Quantitative Structure-Activity Relationship models and using them for virtual screening of chemical libraries to prioritize the compound selection for drug discovery and/or chemical safety assessment. AVAILABILITY: Freely accessible at: http://chembench.mml.unc.edu CONTACT: alex_tropsha@unc.edu

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Year:  2010        PMID： 20889496      PMCID： PMC2982152          DOI： 10.1093/bioinformatics/btq556

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

1.  NIH Molecular Libraries Initiative.

Authors:  Christopher P Austin; Linda S Brady; Thomas R Insel; Francis S Collins
Journal:  Science       Date:  2004-11-12       Impact factor: 47.728

Review 2.  Editorial opinion: chemoinformatics - a ten year update.

Authors:  Frank Brown
Journal:  Curr Opin Drug Discov Devel       Date:  2005-05

3.  QSAR modeling of the blood-brain barrier permeability for diverse organic compounds.

Authors:  Liying Zhang; Hao Zhu; Tudor I Oprea; Alexander Golbraikh; Alexander Tropsha
Journal:  Pharm Res       Date:  2008-06-14       Impact factor: 4.200

4.  Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research.

Authors:  Denis Fourches; Eugene Muratov; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2010-07-26       Impact factor: 4.956

5.  Combinatorial QSAR modeling of P-glycoprotein substrates.

Authors:  Patricia de Cerqueira Lima; Alexander Golbraikh; Scott Oloff; Yunde Xiao; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2006 May-Jun       Impact factor: 4.956

6.  CDK-Taverna: an open workflow environment for cheminformatics.

Authors:  Thomas Kuhn; Egon L Willighagen; Achim Zielesny; Christoph Steinbeck
Journal:  BMC Bioinformatics       Date:  2010-03-29       Impact factor: 3.169

7.  DrugBank: a knowledgebase for drugs, drug actions and drug targets.

Authors:  David S Wishart; Craig Knox; An Chi Guo; Dean Cheng; Savita Shrivastava; Dan Tzur; Bijaya Gautam; Murtaza Hassanali
Journal:  Nucleic Acids Res       Date:  2007-11-29       Impact factor: 16.971
  7 in total
  28 in total

1.  The perspectives of computational chemistry modeling.

Authors:  Igor V Tetko
Journal:  J Comput Aided Mol Des       Date:  2011-12-11       Impact factor: 3.686

2.  Chembench: A Publicly Accessible, Integrated Cheminformatics Portal.

Authors:  Stephen J Capuzzi; Ian Sang-June Kim; Wai In Lam; Thomas E Thornton; Eugene N Muratov; Diane Pozefsky; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2017-01-19       Impact factor: 4.956

3.  Computer-Aided Discovery and Characterization of Novel Ebola Virus Inhibitors.

Authors:  Stephen J Capuzzi; Wei Sun; Eugene N Muratov; Carles Martínez-Romero; Shihua He; Wenjun Zhu; Hao Li; Gregory Tawa; Ethan G Fisher; Miao Xu; Paul Shinn; Xiangguo Qiu; Adolfo García-Sastre; Wei Zheng; Alexander Tropsha
Journal:  J Med Chem       Date:  2018-04-17       Impact factor: 7.446

4.  Toxicokinetic Triage for Environmental Chemicals.

Authors:  John F Wambaugh; Barbara A Wetmore; Robert Pearce; Cory Strope; Rocky Goldsmith; James P Sluka; Alexander Sedykh; Alex Tropsha; Sieto Bosgra; Imran Shah; Richard Judson; Russell S Thomas; R Woodrow Setzer
Journal:  Toxicol Sci       Date:  2015-06-16       Impact factor: 4.849

5.  Predicting Nano-Bio Interactions by Integrating Nanoparticle Libraries and Quantitative Nanostructure Activity Relationship Modeling.

Authors:  Wenyi Wang; Alexander Sedykh; Hainan Sun; Linlin Zhao; Daniel P Russo; Hongyu Zhou; Bing Yan; Hao Zhu
Journal:  ACS Nano       Date:  2017-11-22       Impact factor: 15.881

6.  Predictive Modeling of Estrogen Receptor Binding Agents Using Advanced Cheminformatics Tools and Massive Public Data.

Authors:  Kathryn Ribay; Marlene T Kim; Wenyi Wang; Daniel Pinolini; Hao Zhu
Journal:  Front Environ Sci       Date:  2016-03-08

7.  Developing Enhanced Blood-Brain Barrier Permeability Models: Integrating External Bio-Assay Data in QSAR Modeling.

Authors:  Wenyi Wang; Marlene T Kim; Alexander Sedykh; Hao Zhu
Journal:  Pharm Res       Date:  2015-04-11       Impact factor: 4.200

Review 8.  The Next Era: Deep Learning in Pharmaceutical Research.

Authors:  Sean Ekins
Journal:  Pharm Res       Date:  2016-09-06       Impact factor: 4.200

9.  Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

Authors:  Jie Xia; Ermias Lemma Tilahun; Terry-Elinor Reid; Liangren Zhang; Xiang Simon Wang
Journal:  Methods       Date:  2014-12-03       Impact factor: 3.608

10.  Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches.

Authors:  Liying Zhang; Alexander Sedykh; Ashutosh Tripathi; Hao Zhu; Antreas Afantitis; Varnavas D Mouchlis; Georgia Melagraki; Ivan Rusyn; Alexander Tropsha
Journal:  Toxicol Appl Pharmacol       Date:  2013-05-23       Impact factor: 4.219
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