Literature DB >> 28045544

Chembench: A Publicly Accessible, Integrated Cheminformatics Portal.

Stephen J Capuzzi1, Ian Sang-June Kim1, Wai In Lam1, Thomas E Thornton1, Eugene N Muratov1, Diane Pozefsky1, Alexander Tropsha1.   

Abstract

The enormous increase in the amount of publicly available chemical genomics data and the growing emphasis on data sharing and open science mandates that cheminformaticians also make their models publicly available for broad use by the scientific community. Chembench is one of the first publicly accessible, integrated cheminformatics Web portals. It has been extensively used by researchers from different fields for curation, visualization, analysis, and modeling of chemogenomics data. Since its launch in 2008, Chembench has been accessed more than 1 million times by more than 5000 users from a total of 98 countries. We report on the recent updates and improvements that increase the simplicity of use, computational efficiency, accuracy, and accessibility of a broad range of tools and services for computer-assisted drug design and computational toxicology available on Chembench. Chembench remains freely accessible at https://chembench.mml.unc.edu.

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Year:  2017        PMID: 28045544      PMCID: PMC5720369          DOI: 10.1021/acs.jcim.6b00462

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  29 in total

1.  Novel variable selection quantitative structure--property relationship approach based on the k-nearest-neighbor principle

Authors: 
Journal:  J Chem Inf Comput Sci       Date:  2000-01

2.  Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis.

Authors:  Hao Zhu; Alexander Tropsha; Denis Fourches; Alexandre Varnek; Ester Papa; Paola Gramatica; Tomas Oberg; Phuong Dao; Artem Cherkasov; Igor V Tetko
Journal:  J Chem Inf Model       Date:  2008-03-01       Impact factor: 4.956

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.  Data set modelability by QSAR.

Authors:  Alexander Golbraikh; Eugene Muratov; Denis Fourches; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2014-01-08       Impact factor: 4.956

5.  Human intestinal transporter database: QSAR modeling and virtual profiling of drug uptake, efflux and interactions.

Authors:  Alexander Sedykh; Denis Fourches; Jianmin Duan; Oliver Hucke; Michel Garneau; Hao Zhu; Pierre Bonneau; Alexander Tropsha
Journal:  Pharm Res       Date:  2012-12-27       Impact factor: 4.200

6.  The use of pseudo-equilibrium constant affords improved QSAR models of human plasma protein binding.

Authors:  Xiang-Wei Zhu; Alexander Sedykh; Hao Zhu; Shu-Shen Liu; Alexander Tropsha
Journal:  Pharm Res       Date:  2013-04-09       Impact factor: 4.200

7.  Critical evaluation of human oral bioavailability for pharmaceutical drugs by using various cheminformatics approaches.

Authors:  Marlene T Kim; Alexander Sedykh; Suman K Chakravarti; Roustem D Saiakhov; Hao Zhu
Journal:  Pharm Res       Date:  2013-12-03       Impact factor: 4.200

8.  JSME: a free molecule editor in JavaScript.

Authors:  Bruno Bienfait; Peter Ertl
Journal:  J Cheminform       Date:  2013-05-21       Impact factor: 5.514

9.  Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information.

Authors:  Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Matthias Rupp; Wolfram Teetz; Stefan Brandmaier; Ahmed Abdelaziz; Volodymyr V Prokopenko; Vsevolod Y Tanchuk; Roberto Todeschini; Alexandre Varnek; Gilles Marcou; Peter Ertl; Vladimir Potemkin; Maria Grishina; Johann Gasteiger; Christof Schwab; Igor I Baskin; Vladimir A Palyulin; Eugene V Radchenko; William J Welsh; Vladyslav Kholodovych; Dmitriy Chekmarev; Artem Cherkasov; Joao Aires-de-Sousa; Qing-You Zhang; Andreas Bender; Florian Nigsch; Luc Patiny; Antony Williams; Valery Tkachenko; Igor V Tetko
Journal:  J Comput Aided Mol Des       Date:  2011-06-10       Impact factor: 3.686

10.  PubChem BioAssay: 2014 update.

Authors:  Yanli Wang; Tugba Suzek; Jian Zhang; Jiyao Wang; Siqian He; Tiejun Cheng; Benjamin A Shoemaker; Asta Gindulyte; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2013-11-05       Impact factor: 16.971

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  16 in total

1.  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

2.  Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

Authors:  Stephen J Capuzzi; Thomas E Thornton; Kammy Liu; Nancy Baker; Wai In Lam; Colin P O'Banion; Eugene N Muratov; Diane Pozefsky; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2018-01-19       Impact factor: 4.956

3.  Influence of feature rankers in the construction of molecular activity prediction models.

Authors:  Gonzalo Cerruela-García; José Pérez-Parra Toledano; Aída de Haro-García; Nicolás García-Pedrajas
Journal:  J Comput Aided Mol Des       Date:  2019-12-31       Impact factor: 3.686

4.  Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models.

Authors:  Vinicius M Alves; Alexander Golbraikh; Stephen J Capuzzi; Kammy Liu; Wai In Lam; Daniel Robert Korn; Diane Pozefsky; Carolina Horta Andrade; Eugene N Muratov; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2018-06-13       Impact factor: 4.956

5.  Opportunities and challenges using artificial intelligence in ADME/Tox.

Authors:  Barun Bhhatarai; W Patrick Walters; Cornelis E C A Hop; Guido Lanza; Sean Ekins
Journal:  Nat Mater       Date:  2019-05       Impact factor: 43.841

6.  PreS/MD: Predictor of Sensitization Hazard for Chemical Substances Released From Medical Devices.

Authors:  Vinicius M Alves; Joyce V B Borba; Rodolpho C Braga; Daniel R Korn; Nicole Kleinstreuer; Kevin Causey; Alexander Tropsha; Diego Rua; Eugene N Muratov
Journal:  Toxicol Sci       Date:  2022-09-24       Impact factor: 4.109

7.  Allosteric Binders of ACE2 Are Promising Anti-SARS-CoV-2 Agents.

Authors:  Joshua E Hochuli; Sankalp Jain; Cleber Melo-Filho; Zoe L Sessions; Tesia Bobrowski; Jun Choe; Johnny Zheng; Richard Eastman; Daniel C Talley; Ganesha Rai; Anton Simeonov; Alexander Tropsha; Eugene N Muratov; Bolormaa Baljinnyam; Alexey V Zakharov
Journal:  ACS Pharmacol Transl Sci       Date:  2022-06-22

Review 8.  In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts.

Authors:  Hongbin Yang; Lixia Sun; Weihua Li; Guixia Liu; Yun Tang
Journal:  Front Chem       Date:  2018-02-20       Impact factor: 5.221

9.  ChemSAR: an online pipelining platform for molecular SAR modeling.

Authors:  Jie Dong; Zhi-Jiang Yao; Min-Feng Zhu; Ning-Ning Wang; Ben Lu; Alex F Chen; Ai-Ping Lu; Hongyu Miao; Wen-Bin Zeng; Dong-Sheng Cao
Journal:  J Cheminform       Date:  2017-05-04       Impact factor: 5.514

10.  A Novel Small-Molecule Inhibitor of Endosomal TLRs Reduces Inflammation and Alleviates Autoimmune Disease Symptoms in Murine Models.

Authors:  Mahesh Chandra Patra; Asma Achek; Gi-Young Kim; Suresh Panneerselvam; Hyeon-Jun Shin; Wook-Yong Baek; Wang Hee Lee; June Sung; Uisuk Jeong; Eun-Young Cho; Wook Kim; Eunha Kim; Chang-Hee Suh; Sangdun Choi
Journal:  Cells       Date:  2020-07-09       Impact factor: 6.600

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