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Akademický článek

Diversity-Oriented Synthesis of a Library of Substituted Tetrahydropyrones Using Oxidative Carbon-Hydrogen Bond Activation and Click Chemistry

Autor: Paul E. Floreancig, Lei Liu, Peter Wipf, Matthew G. LaPorte, Ramy Farid, Nilesh Zaware

Publikováno v: Molecules, Vol 16, Iss 5, Pp 3648-3662 (2011)

Eighteen (2RS,6RS)-2-(4-methoxyphenyl)-6-(substituted ethyl)dihydro-2H-pyran-4(3H)ones were synthesized via a DDQ-mediated oxidative carbon-hydrogen bond activation reaction. Fourteen of these tetrahydropyrans were substituted with triazoles readily

Externí odkaz: https://doaj.org/article/88d4fe88b25c421ebcc328cfb63e2439

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Controlling Chaotic Systems via Time-delayed Control

Autor: Ramy Farid, Abdul-Azim Ibrahim, Belal Abou-Zalam

Publikováno v: International Journal of Computers and Communications. 15:44-49

Based on Lyapunov stabilization theory, this paper proposes a proportional plus integral time-delayed controller to stabilize unstable equilibrium points (UPOs) embedded in chaotic attractors. The criterion is successfully applied to the classic Chua

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::20d8b39a6022d4b205cdab7a5f0099a8
https://doi.org/10.46300/91013.2021.15.8

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A novel inhibitor of active protein kinase G attenuates chronic inflammatory and osteoarthritic pain

Autor: Donald W. Landry, Yuli Xie, Ramy Farid, Mary Nkamany, Nelson Sofoluke, Shi-Xian Deng, Jeremy R. Greenwood, Ying-Ju Sung, Richard T. Ambron

Publikováno v: Pain

Supplemental Digital Content is Available in the Text. A novel and potent protein kinase G-1α (PKG-1α) inhibitor is used to demonstrate the important roles of PKG in capsaicin-induced acute pain and in persistent inflammatory pain.
Activating

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e5fc11462d50df293dace13ea01ff50a
http://europepmc.org/articles/PMC5402717

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A Free Energy Perturbation Approach to Estimate the Intrinsic Solubilities of Drug-like Small Molecules

Autor: Byungchan Kim, Jeremy R. Greenwood, Matt Wirtala, Sayan Mondal, Gary Tresadern, Robert Abel, Thomas Steinbrecher, Craig E. Masse, Joe Kaus, Ramy Farid, Lingle Wang

Optimizing the solubility of small molecules is important in a wide variety of contexts, including in drug discovery where the optimization of aqueous solubility is often crucial to achieve oral bioavailability. In such a context, solubility optimiza

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1a58a17bf37e15beebc229506dab5a46
https://doi.org/10.26434/chemrxiv.10263077

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Modeling the value of predictive affinity scoring in preclinical drug discovery

Autor: Lingle Wang, Eric S. Manas, Robert Abel, Richard A. Friesner, Ramy Farid

Publikováno v: Current opinion in structural biology. 52

Drug discovery is widely recognized to be a difficult and costly activity in large part due to the challenge of identifying chemical matter which simultaneously optimizes multiple properties, one of which is affinity for the primary biological target

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1523e8ad2995b1268677fcdfa10adebc
https://pubmed.ncbi.nlm.nih.gov/30321805

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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Publikováno v: Journal of the American Chemical Society, vol 137, iss 7
Wang, L; Wu, Y; Deng, Y; Kim, B; Pierce, L; Krilov, G; et al.(2015). Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society, 137(7), 2695-2703. doi: 10.1021/ja512751q. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/5061663w

© 2015 American Chemical Society. Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::773d1836a8ebda0977ca7d9384d08fcb
https://doi.org/10.1021/ja512751q

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Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring

Autor: Ramy Farid, Edward Harder, Jeremy R. Greenwood, Kenneth W. Borrelli, Tyler Day, Kai Zhu, Robert Abel

Publikováno v: Journal of Chemical Information and Modeling. 54:1932-1940

Although many popular docking programs include a facility to account for covalent ligands, large-scale systematic docking validation studies of covalent inhibitors have been sparse. In this paper, we present the development and validation of a novel

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cc6bd8619274f1a5d08e8fa4baf62a22
https://doi.org/10.1021/ci500118s

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WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking

Autor: Christopher D. Schmitz, Ramy Farid, Ivan Tubert-Brohman, Robert B. Murphy, Nicholas A. Boyles, Ramakrishna Annabhimoju, Matthew P. Repasky, Jeremy R. Greenwood, Steven V. Jerome, Richard A. Friesner, Robert Abel

Publikováno v: Journal of medicinal chemistry. 59(9)

We have developed a new methodology for protein–ligand docking and scoring, WScore, incorporating a flexible description of explicit water molecules. The locations and thermodynamics of the waters are derived from a WaterMap molecular dynamics simu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::066638d2fb98767e22d0d42c05642b09
https://pubmed.ncbi.nlm.nih.gov/27054459

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The translocation kinetics of antibiotics through porin OmpC: Insights from structure-based solvation mapping using WaterMap

Autor: Sarah Williams, Robert A. Pearlstein, Ramy Farid, Que-Tien Tran, Gul Erdemli

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 81:291-299

Poor permeability of the lipopolysaccharide-based outer membrane of Gram-negative bacteria is compensated by the existence of protein channels (porins) that selectively admit low molecular weight substrates, including many antibiotics. Improved under

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f71fe8640b709f6de7b0aea1c2838329
https://doi.org/10.1002/prot.24185

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Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

Autor: Kenneth L. Ho, Ramy Farid, Jeffrey A. Bell

Publikováno v: Acta Crystallographica Section D: Biological Crystallography

All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fada3f7ecde95b06e05bf7a39e4163ae
http://europepmc.org/articles/PMC3413210

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