Corrigendum to 'Optimizing active learning for free energy Calculations' [Artificial Intelligence in the Life Sciences, 2 (2022) 100050]

Autor: James Thompson, W Patrick Walters, Jianwen A Feng, Nicolas A Pabon, Hongcheng Xu, Brian B Goldman, Demetri Moustakas, Molly Schmidt, Forrest York

Publikováno v: Artificial Intelligence in the Life Sciences, Vol 3, Iss , Pp 100074- (2023)

Externí odkaz: https://doaj.org/article/38729ea392e043bb89ec2e372de9b12e

chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery

Autor: Man-Ling Lee, Ignacio Aliagas, Jianwen A. Feng, Thomas Gabriel, T. J. O’Donnell, Benjamin D. Sellers, Bernd Wiswedel, Alberto Gobbi

Publikováno v: Journal of Cheminformatics, Vol 9, Iss 1, Pp 1-14 (2017)

Abstract Background Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of comman

Externí odkaz: https://doaj.org/article/edfb9c52e3044076802ecdada87add4f

An integrated suite of modeling tools that empower scientists in structure- and property-based drug design

Autor: Jeff Blaney, Man-Ling Lee, Alberto Gobbi, Ignacio Aliagas, Vickie Tsui, Philippe Bergeron, Erin K. Bradley, Daniel F. Ortwine, Michael F. T. Koehler, Jianwen A. Feng, Johnny Wu

Publikováno v: Journal of Computer-Aided Molecular Design. 29:511-523

Structure- and property-based drug design is an integral part of modern drug discovery, enabling the design of compounds aimed at improving potency and selectivity. However, building molecules using desktop modeling tools can easily lead to poor desi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9389847212e31c57ba321ed8ae96c49a
https://doi.org/10.1007/s10822-015-9845-4

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

Autor: John D. Chodera, Jianwen A. Feng, Ariën S. Rustenburg, Baiwei Lin, Justin Dancer, Daniel F. Ortwine, David L. Mobley

Publikováno v: Rustenburg, AS; Dancer, J; Lin, B; Feng, JA; Ortwine, DF; Mobley, DL; et al.(2016). Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 30(11), 945-958. doi: 10.1007/s10822-016-9971-7. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/3557d1tc

Small molecule distribution coefficients between immiscible nonaqueuous and aqueous phases—such as cyclohexane and water—measure the degree to which small molecules prefer one phase over another at a given pH. As distribution coefficients capture

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::94038553481c0b41f55e67f038595321
http://www.escholarship.org/uc/item/3557d1tc

Back pocket flexibility provides group II p21-activated kinase (PAK) selectivity for type I 1/2 kinase inhibitors

Autor: Yisong Xiao, Yamin Zhang, Christine Tam, David A. Roberts, Lori Friedman, Adrian Kotey, Hartmut Koeppen, Antonio G. DiPasquale, Marcia Belvin, Jason Burch, Angela Oh, Weiru Wang, Karen Lyle, Jason Boggs, Lionel Rouge, Klaus P. Hoeflich, Robert Mintzer, Steven T. Staben, Amy E. Young, Jianwen A. Feng, Joachim Rudolph, Ching-ching Chua, Christopher E. Heise, Hai-Feng Cui

Publikováno v: Journal of medicinal chemistry. 57(3)

Structure-based methods were used to design a potent and highly selective group II p21-activated kinase (PAK) inhibitor with a novel binding mode, compound 17. Hydrophobic interactions within a lipophilic pocket past the methionine gatekeeper of grou

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::245fbcc6094e3c442d4f7457a0aa98fd
https://pubmed.ncbi.nlm.nih.gov/24432870