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The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.

Methods in molecular biology (Clifton, N.J.)

Kotera M, Hirakawa M, Tokimatsu T, Goto S, Kanehisa M.
PMID: 22130871
Methods Mol Biol. 2012;802:19-39. doi: 10.1007/978-1-61779-400-1_2.

In this chapter, we demonstrate the usability of the KEGG (Kyoto encyclopedia of genes and genomes) databases and tools, especially focusing on the visualization of the omics data. The desktop application KegArray and many Web-based tools are tightly integrated...

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Kotera M, Hirakawa M, Tokimatsu T, et al. The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol Biol. 2012;802:19-39doi: 10.1007/978-1-61779-400-1_2.
Kotera, M., Hirakawa, M., Tokimatsu, T., Goto, S., & Kanehisa, M. (2012). The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods in molecular biology (Clifton, N.J.), 80219-39. https://doi.org/10.1007/978-1-61779-400-1_2
Kotera, Masaaki, et al. "The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals." Methods in molecular biology (Clifton, N.J.) vol. 802 (2012): 19-39. doi: https://doi.org/10.1007/978-1-61779-400-1_2
Kotera M, Hirakawa M, Tokimatsu T, Goto S, Kanehisa M. The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol Biol. 2012;802:19-39. doi: 10.1007/978-1-61779-400-1_2. PMID: 22130871.
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The current state of drug discovery and a potential role for NMR metabolomics.

Journal of medicinal chemistry

Powers R.
PMID: 24588729
J Med Chem. 2014 Jul 24;57(14):5860-70. doi: 10.1021/jm401803b. Epub 2014 Mar 03.

The pharmaceutical industry has significantly contributed to improving human health. Drugs have been attributed to both increasing life expectancy and decreasing health care costs. Unfortunately, there has been a recent decline in the creativity and productivity of the pharmaceutical...

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Powers R. The current state of drug discovery and a potential role for NMR metabolomics. J Med Chem. 2014;57(14):5860-70doi: 10.1021/jm401803b.
Powers, R. (2014). The current state of drug discovery and a potential role for NMR metabolomics. Journal of medicinal chemistry, 57(14), 5860-70. https://doi.org/10.1021/jm401803b
Powers, Robert. "The current state of drug discovery and a potential role for NMR metabolomics." Journal of medicinal chemistry vol. 57,14 (2014): 5860-70. doi: https://doi.org/10.1021/jm401803b
Powers R. The current state of drug discovery and a potential role for NMR metabolomics. J Med Chem. 2014 Jul 24;57(14):5860-70. doi: 10.1021/jm401803b. Epub 2014 Mar 03. PMID: 24588729; PMCID: PMC4324437.
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Pharmaceutical structure montages as catalysts for design and discovery.

Future medicinal chemistry

Njarðarson JT.
PMID: 22650237
Future Med Chem. 2012 May;4(8):951-4. doi: 10.4155/fmc.12.30.

Majority of pharmaceuticals are small molecule organic compounds. Their structures are most effectively described and communicated using the graphical language of organic chemistry. A few years ago we decided to harness this powerful language to create new educational tools...

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Njarðarson JT. Pharmaceutical structure montages as catalysts for design and discovery. Future Med Chem. 2012;4(8):951-4doi: 10.4155/fmc.12.30.
Njarðarson, J. T. (2012). Pharmaceutical structure montages as catalysts for design and discovery. Future medicinal chemistry, 4(8), 951-4. https://doi.org/10.4155/fmc.12.30
Njarðarson, Jon T. "Pharmaceutical structure montages as catalysts for design and discovery." Future medicinal chemistry vol. 4,8 (2012): 951-4. doi: https://doi.org/10.4155/fmc.12.30
Njarðarson JT. Pharmaceutical structure montages as catalysts for design and discovery. Future Med Chem. 2012 May;4(8):951-4. doi: 10.4155/fmc.12.30. PMID: 22650237.
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Going further than Lipinski's rule in drug design.

Expert opinion on drug discovery

Walters WP.
PMID: 22468912
Expert Opin Drug Discov. 2012 Feb;7(2):99-107. doi: 10.1517/17460441.2012.648612. Epub 2012 Jan 13.

INTRODUCTION: Lipinski's 1997 publication of the 'Rule of 5' (Ro5) was one of the most influential recent medicinal chemistry publications. In the almost 15 years since the publication of the original Ro5 paper, multiple groups have refined and expanded...

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Walters WP. Going further than Lipinski's rule in drug design. Expert Opin Drug Discov. 2012;7(2):99-107doi: 10.1517/17460441.2012.648612.
Walters, W. P. (2012). Going further than Lipinski's rule in drug design. Expert opinion on drug discovery, 7(2), 99-107. https://doi.org/10.1517/17460441.2012.648612
Walters, W Patrick. "Going further than Lipinski's rule in drug design." Expert opinion on drug discovery vol. 7,2 (2012): 99-107. doi: https://doi.org/10.1517/17460441.2012.648612
Walters WP. Going further than Lipinski's rule in drug design. Expert Opin Drug Discov. 2012 Feb;7(2):99-107. doi: 10.1517/17460441.2012.648612. Epub 2012 Jan 13. PMID: 22468912.
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Life cycle analysis within pharmaceutical process optimization and intensification: case study of active pharmaceutical ingredient production.

ChemSusChem

Ott D, Kralisch D, Denčić I, Hessel V, Laribi Y, Perrichon PD, Berguerand C, Kiwi-Minsker L, Loeb P.
PMID: 25251078
ChemSusChem. 2014 Dec;7(12):3521-33. doi: 10.1002/cssc.201402313. Epub 2014 Sep 22.

As the demand for new drugs is rising, the pharmaceutical industry faces the quest of shortening development time, and thus, reducing the time to market. Environmental aspects typically still play a minor role within the early phase of process...

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Ott D, Kralisch D, Denčić I, et al. Life cycle analysis within pharmaceutical process optimization and intensification: case study of active pharmaceutical ingredient production. ChemSusChem. 2014;7(12):3521-33doi: 10.1002/cssc.201402313.
Ott, D., Kralisch, D., Denčić, I., Hessel, V., Laribi, Y., Perrichon, P. D., Berguerand, C., Kiwi-Minsker, L., & Loeb, P. (2014). Life cycle analysis within pharmaceutical process optimization and intensification: case study of active pharmaceutical ingredient production. ChemSusChem, 7(12), 3521-33. https://doi.org/10.1002/cssc.201402313
Ott, Denise, et al. "Life cycle analysis within pharmaceutical process optimization and intensification: case study of active pharmaceutical ingredient production." ChemSusChem vol. 7,12 (2014): 3521-33. doi: https://doi.org/10.1002/cssc.201402313
Ott D, Kralisch D, Denčić I, Hessel V, Laribi Y, Perrichon PD, Berguerand C, Kiwi-Minsker L, Loeb P. Life cycle analysis within pharmaceutical process optimization and intensification: case study of active pharmaceutical ingredient production. ChemSusChem. 2014 Dec;7(12):3521-33. doi: 10.1002/cssc.201402313. Epub 2014 Sep 22. PMID: 25251078.
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Determination of phosphodiesterase-5 inhibitors and analogs using high-performance liquid chromatography with ultraviolet detection.

Journal of chromatographic science

Nickum EA, Flurer CL.
PMID: 24668043
J Chromatogr Sci. 2015 Jan;53(1):38-46. doi: 10.1093/chromsci/bmu010. Epub 2014 Mar 24.

A considerable number of erectile dysfunction products, and dietary supplements suspected of containing phosphodiesterase-5 (PDE-5) inhibitors, have been analyzed by the US Food and Drug Administration. Often these samples are found to contain the approved active pharmaceutical ingredients (APIs)...

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Nickum EA, Flurer CL. Determination of phosphodiesterase-5 inhibitors and analogs using high-performance liquid chromatography with ultraviolet detection. J Chromatogr Sci. 2014;53(1):38-46doi: 10.1093/chromsci/bmu010.
Nickum, E. A., & Flurer, C. L. (2015). Determination of phosphodiesterase-5 inhibitors and analogs using high-performance liquid chromatography with ultraviolet detection. Journal of chromatographic science, 53(1), 38-46. https://doi.org/10.1093/chromsci/bmu010
Nickum, Elisa A, and Flurer, Cheryl L. "Determination of phosphodiesterase-5 inhibitors and analogs using high-performance liquid chromatography with ultraviolet detection." Journal of chromatographic science vol. 53,1 (2015): 38-46. doi: https://doi.org/10.1093/chromsci/bmu010
Nickum EA, Flurer CL. Determination of phosphodiesterase-5 inhibitors and analogs using high-performance liquid chromatography with ultraviolet detection. J Chromatogr Sci. 2015 Jan;53(1):38-46. doi: 10.1093/chromsci/bmu010. Epub 2014 Mar 24. PMID: 24668043.
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Advances in dissolution instrumentation and their practical applications.

Drug development and industrial pharmacy

Culen M, Dohnal J.
PMID: 24093430
Drug Dev Ind Pharm. 2014 Oct;40(10):1277-82. doi: 10.3109/03639045.2013.841184. Epub 2013 Oct 04.

The rising demands on discriminatory and prediction abilities of dissolution methods and the increasing complexity of new drug products are the main driving forces of the progress in this field. The research moves forward as imperfections and shortcomings of...

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Culen M, Dohnal J. Advances in dissolution instrumentation and their practical applications. Drug Dev Ind Pharm. 2013;40(10):1277-82doi: 10.3109/03639045.2013.841184.
Culen, M., & Dohnal, J. (2014). Advances in dissolution instrumentation and their practical applications. Drug development and industrial pharmacy, 40(10), 1277-82. https://doi.org/10.3109/03639045.2013.841184
Culen, Martin, and Dohnal, Jiri. "Advances in dissolution instrumentation and their practical applications." Drug development and industrial pharmacy vol. 40,10 (2014): 1277-82. doi: https://doi.org/10.3109/03639045.2013.841184
Culen M, Dohnal J. Advances in dissolution instrumentation and their practical applications. Drug Dev Ind Pharm. 2014 Oct;40(10):1277-82. doi: 10.3109/03639045.2013.841184. Epub 2013 Oct 04. PMID: 24093430.
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Editorial.

Journal of pharmaceutical sciences

Borchardt RT.
PMID: 29421213
J Pharm Sci. 2018 Apr;107(4):957. doi: 10.1016/j.xphs.2018.01.022. Epub 2018 Feb 05.

No abstract available.

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Borchardt RT. Editorial. J Pharm Sci. 2018;107(4):957doi: 10.1016/j.xphs.2018.01.022.
Borchardt, R. T. (2018). Editorial. Journal of pharmaceutical sciences, 107(4), 957. https://doi.org/10.1016/j.xphs.2018.01.022
Borchardt, Ronald T. "Editorial." Journal of pharmaceutical sciences vol. 107,4 (2018): 957. doi: https://doi.org/10.1016/j.xphs.2018.01.022
Borchardt RT. Editorial. J Pharm Sci. 2018 Apr;107(4):957. doi: 10.1016/j.xphs.2018.01.022. Epub 2018 Feb 05. PMID: 29421213.
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Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects.

Journal of chemical information and modeling

Fernandez M, Ban F, Woo G, Isaev O, Perez C, Fokin V, Tropsha A, Cherkasov A.
PMID: 30767528
J Chem Inf Model. 2019 Apr 22;59(4):1306-1313. doi: 10.1021/acs.jcim.8b00747. Epub 2019 Feb 28.

In recent years, the field of quantitative structure-activity/property relationship (QSAR/QSPR) modeling has developed into a stable technology capable of reliably predicting new bioactive molecules. With the availability of inexpensive commercial sources of both synthetic chemicals and bioactivity assays, a...

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Fernandez M, Ban F, Woo G, et al. Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. J Chem Inf Model. 2019;59(4):1306-1313doi: 10.1021/acs.jcim.8b00747.
Fernandez, M., Ban, F., Woo, G., Isaev, O., Perez, C., Fokin, V., Tropsha, A., & Cherkasov, A. (2019). Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. Journal of chemical information and modeling, 59(4), 1306-1313. https://doi.org/10.1021/acs.jcim.8b00747
Fernandez, Michael, et al. "Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects." Journal of chemical information and modeling vol. 59,4 (2019): 1306-1313. doi: https://doi.org/10.1021/acs.jcim.8b00747
Fernandez M, Ban F, Woo G, Isaev O, Perez C, Fokin V, Tropsha A, Cherkasov A. Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. J Chem Inf Model. 2019 Apr 22;59(4):1306-1313. doi: 10.1021/acs.jcim.8b00747. Epub 2019 Feb 28. PMID: 30767528.
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Screening for new pharmaceutical solid forms using mechanochemistry: A practical guide.

Advanced drug delivery reviews

Hasa D, Jones W.
PMID: 28478084
Adv Drug Deliv Rev. 2017 Aug 01;117:147-161. doi: 10.1016/j.addr.2017.05.001. Epub 2017 May 03.

Within the pharmaceutical industry, and elsewhere, the screening for new solid forms is a mandatory exercise for both existing and new chemical entities. This contribution focuses on mechanochemistry as a versatile approach for discovering new and alternative solid forms....

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Hasa D, Jones W. Screening for new pharmaceutical solid forms using mechanochemistry: A practical guide. Adv Drug Deliv Rev. 2017;117:147-161doi: 10.1016/j.addr.2017.05.001.
Hasa, D., & Jones, W. (2017). Screening for new pharmaceutical solid forms using mechanochemistry: A practical guide. Advanced drug delivery reviews, 117147-161. https://doi.org/10.1016/j.addr.2017.05.001
Hasa, Dritan, and Jones, William. "Screening for new pharmaceutical solid forms using mechanochemistry: A practical guide." Advanced drug delivery reviews vol. 117 (2017): 147-161. doi: https://doi.org/10.1016/j.addr.2017.05.001
Hasa D, Jones W. Screening for new pharmaceutical solid forms using mechanochemistry: A practical guide. Adv Drug Deliv Rev. 2017 Aug 01;117:147-161. doi: 10.1016/j.addr.2017.05.001. Epub 2017 May 03. PMID: 28478084.
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Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

Expert opinion on drug discovery

Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A.
PMID: 28602100
Expert Opin Drug Discov. 2017 Aug;12(8):757-767. doi: 10.1080/17460441.2017.1339032. Epub 2017 Jun 12.

INTRODUCTION: ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration...

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Nowotka MM, Gaulton A, Mendez D, et al. Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. Expert Opin Drug Discov. 2017;12(8):757-767doi: 10.1080/17460441.2017.1339032.
Nowotka, M. M., Gaulton, A., Mendez, D., Bento, A. P., Hersey, A., & Leach, A. (2017). Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. Expert opinion on drug discovery, 12(8), 757-767. https://doi.org/10.1080/17460441.2017.1339032
Nowotka, Michał M, et al. "Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery." Expert opinion on drug discovery vol. 12,8 (2017): 757-767. doi: https://doi.org/10.1080/17460441.2017.1339032
Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A. Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. Expert Opin Drug Discov. 2017 Aug;12(8):757-767. doi: 10.1080/17460441.2017.1339032. Epub 2017 Jun 12. PMID: 28602100; PMCID: PMC6321761.
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The CSD Drug Subset: The Changing Chemistry and Crystallography of Small Molecule Pharmaceuticals.

Journal of pharmaceutical sciences

Bryant MJ, Black SN, Blade H, Docherty R, Maloney AGP, Taylor SC.
PMID: 30615878
J Pharm Sci. 2019 May;108(5):1655-1662. doi: 10.1016/j.xphs.2018.12.011. Epub 2019 Jan 05.

We report the generation and statistical analysis of the CSD drug subset: a subset of the Cambridge Structural Database (CSD) consisting of every published small-molecule crystal structure containing an approved drug molecule. By making use of InChI matching, a...

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Bryant MJ, Black SN, Blade H, et al. The CSD Drug Subset: The Changing Chemistry and Crystallography of Small Molecule Pharmaceuticals. J Pharm Sci. 2019;108(5):1655-1662doi: 10.1016/j.xphs.2018.12.011.
Bryant, M. J., Black, S. N., Blade, H., Docherty, R., Maloney, A. G. P., & Taylor, S. C. (2019). The CSD Drug Subset: The Changing Chemistry and Crystallography of Small Molecule Pharmaceuticals. Journal of pharmaceutical sciences, 108(5), 1655-1662. https://doi.org/10.1016/j.xphs.2018.12.011
Bryant, Mathew J, et al. "The CSD Drug Subset: The Changing Chemistry and Crystallography of Small Molecule Pharmaceuticals." Journal of pharmaceutical sciences vol. 108,5 (2019): 1655-1662. doi: https://doi.org/10.1016/j.xphs.2018.12.011
Bryant MJ, Black SN, Blade H, Docherty R, Maloney AGP, Taylor SC. The CSD Drug Subset: The Changing Chemistry and Crystallography of Small Molecule Pharmaceuticals. J Pharm Sci. 2019 May;108(5):1655-1662. doi: 10.1016/j.xphs.2018.12.011. Epub 2019 Jan 05. PMID: 30615878.
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Showing 13 to 24 of 80 entries