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8. Young metropolitan Anglo-Jewish masculinities : a qualitative interview study investigating intersectionality between Jewishness, Britishness, and masculinity

Author

Nicholls, Anthony Jeffery Stephen

Abstract

My thesis is an empirical study of young British Jews, exploring their experience of being Jewish, British, and male in society today given the fluid nature of each of these aspects of their identity. As society has changed over the last half century each of these aspects which had normative monocultural taken-for-granted expressions have been repeatedly deconstructed, examined and re-built, and I argue that in the process they have emerged as fluid entities. It is in negotiating these fluid aspects that today's young male Jews ask, what does it mean to be a Jew, what does it mean to be British, and what does it mean to be male as they try to make sense of their lives. The method chosen for this study has been the in-depth interview which I conducted with a sample of 16 interviewees chosen to reflect the diverse range of religiosity, age and intellectual ability which is apparent in the heterogenous nature of the Anglo-Jewish community supplemented with a group discussion. I have produced an interview tool of overlapping coloured discs representing the three aspects I am studying as an aid for the interviewee to think and talk about themselves. I have transcribed the interviews and used constructionist thematic analysis to advance my argument. I argue that Jewishness is constructed between extremes of adherence to halachic requirement on one hand and a Jewishness experienced as cultural affinity to history, family, and tradition without recourse to halacha on the other hand. I argue that Britishness is being experienced between varying degrees of nationalistic localism against cosmopolitan liberalism played out against a backdrop of Britain contrasted with the rest of the world and also London against the rest of Britain. With regard to being male, I have rejected the view that masculinity is constructed in the inherently unstable terms of physicality against intellectualism. Instead, I argue that it is better considered as lying in a range between competitive hegemonic masculinity on the one hand against a cooperative model with which physicality and intellectualism can combine to produce a more stable and emotionally satisfying mode of living. I argue that young Jewish men inhabit a fluid three-dimensional matrix being aware of the pitfalls of particularism, xenophobia, and misogyny as they negotiate their relationships with their families, communities, and wider society to construct their Jewish British masculine identity.

Published
2022

10. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Author

Adams, Paul D, Aertgeerts, Kathleen, Bauer, Cary, Bell, Jeffrey A, Berman, Helen M, Bhat, Talapady N, Blaney, Jeff M, Bolton, Evan, Bricogne, Gerard, Brown, David, Burley, Stephen K, Case, David A, Clark, Kirk L, Darden, Tom, Emsley, Paul, Feher, Victoria A, Feng, Zukang, Groom, Colin R, Harris, Seth F, Hendle, Jorg, Holder, Thomas, Joachimiak, Andrzej, Kleywegt, Gerard J, Krojer, Tobias, Marcotrigiano, Joseph, Mark, Alan E, Markley, John L, Miller, Matthew, Minor, Wladek, Montelione, Gaetano T, Murshudov, Garib, Nakagawa, Atsushi, Nakamura, Haruki, Nicholls, Anthony, Nicklaus, Marc, Nolte, Robert T, Padyana, Anil K, Peishoff, Catherine E, Pieniazek, Susan, Read, Randy J, Shao, Chenghua, Sheriff, Steven, Smart, Oliver, Soisson, Stephen, Spurlino, John, Stouch, Terry, Svobodova, Radka, Tempel, Wolfram, Terwilliger, Thomas C, Tronrud, Dale, Velankar, Sameer, Ward, Suzanna C, Warren, Gregory L, Westbrook, John D, Williams, Pamela, Yang, Huanwang, and Young, Jasmine

Subjects
Inorganic Chemistry, Biochemistry and Cell Biology, Medicinal and Biomolecular Chemistry, Chemical Sciences, Biological Sciences, Generic health relevance, Crystallography, X-Ray, Data Curation, Databases, Protein, Guidelines as Topic, Ligands, Models, Molecular, Protein Conformation, Proteins, Information and Computing Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

Published
2016

11. Orion ® A Cloud‐Native Molecular Design Platform

Author

Sørensen, Jesper, primary, Bannan, Caitlin C., additional, Calabrò, Gaetano, additional, Jain, Varsha, additional, Ovanesyan, Grigory, additional, Smith, Addison, additional, Zhang, She, additional, Bayly, Christopher I., additional, Darden, Tom A., additional, Geballe, Matthew T., additional, LeBard, David N., additional, McGann, Mark, additional, Moon, Joseph B., additional, Muddana, Hari S., additional, Shewmaker, Andrew, additional, LaFon, Jharrod, additional, Tolbert, Robert W., additional, Skillman, A. Geoffrey, additional, and Nicholls, Anthony, additional

Published
2024
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30. Crystal Structure Prediction of Drug Molecules in the Cloud: A Collaborative Blind Challenge Study

Author

Bannan, Caitlin C., Ovanesyan, Grigory, Darden, Thomas A., Graves, Alan P., Edge, Colin M., Russo, Luca, Copley, Royston C. B., Manas, Eric, Skillman, A. Geoffrey, Nicholls, Anthony, and Muddana, Hari S.

Abstract

Understanding the risk of multiple stable crystal polymorphs for a drug is a vital part of drug formulation and development. Computational crystal structure prediction (CSP) is a valuable tool for efficiently determining this polymorph risk. Improving the computational cost of these protocols could make polymorph screens accessible at an earlier stage of the drug discovery process. To address this need, OpenEye, Cadence Molecular Sciences (OE) partnered with GSK to organize a series of blind challenges to improve OE’s automated CSP protocol. The protocol evolved over six blind challenges, increasing in difficulty, where GSK provided minimal information about each molecule and OE predicted the low energy crystal structures. Beginning with any representation of the molecule (e.g., SMILES), OE predicted a list of possible crystal structures and ranked them with enthalpies or free energies from quantum chemical (QC) calculations. The protocol leveraged the Orion Cloud platform with highly parallelizable calculations and short wall clock times. OE’s blind predictions agreed with GSK’s experimental structures for five out of six molecules with an RMSD20 under 0.25 Å (0.5 Å for a monohydrate). The conformer was revealed for the final challenge, and OE was able to predict the crystal structure after adapting the protocol.

Published
2025
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45. Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory

Author

Tannor, David J., Marten, Bryan, Murphy, Robert, Friesner, Richard A., Sitkoff, Doree, Nicholls, Anthony, Ringnalda, Murco, Goddard, William A., III, and Honig, Barry

Subjects
Solvation -- Research, Gibbs' free energy -- Research, Chemistry
Abstract

A combination of high-level ab initio quantum mechanics and continuum dielectric theory helps evaluate the solvation free energies of organic solutes in water. Gas-phase charge distributions are obtained by employing correlated wave functions at the valence bond/perfect pairing level. These charge distributions help derive the solvation energies. Application of this method for 29 molecules produces an average error of 0.6 kcal/mol for solvation energies, however theoretical predictions significantly differ from experimental observation of solvation energies for methylated and unmethylated primary amines and amides.

Published
1994

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