■ Abstract Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more pro- teins of known structure (templates). The prediction process consists of fold assign- ment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are in- creasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are nec- essary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.

Comparative protein structure modeling of genes and genomes

The Wretched of the Earth

Preface Introduction: Traditions of Nationhood in France and Germany I. The Institution of Citizenship 1. Citizenship as Social Closure 2. The French Revolution and the Invention of National Citizenship 3. State, State-System, and Citizenship in Germany II. Defining The Citizenry: The Bounds of Belonging 4. Citizenship and Naturalization in France and Germany 5. Migrants into Citizens: The Crystallization of Jus Soli in Late-Nineteenth-Century France 6. The Citizenry as Community of Descent: The Nationalization of Citizenship in Wilhelmine Germany 7. \"Etre Francais, Cela se Merite\": Immigration and the Politics of Citizenship in France in the 1980s 8. Continuities in the German Politics of Citizenship Conclusion Notes Bibliography Index

Citizenship and Nationhood in France and Germany.

Culture and Imperialism

Citizen and Subject: Contemporary Africa and the legacy of late colonialism

Making a World after Empire: The Bandung Moment and Its Political Afterlives

The binding of invariant chain to major histocompatibility complex (MHC) proteins is an important step in processing of MHC class II proteins and in antigen presentation. The question of how invariant chain can bind to all MHC class II proteins is central to understanding these processes. We have employed molecular modeling to predict the structure of class II-associated invariant chain peptide (CLIP)-MHC protein complexes and to ask whether the predicted mode of association could be general across all MHC class II proteins. CLIP fits identically into the MHC class II alleles HLA-DR3, I-Ak, I-Au, and I-Ad, with a consistent pattern of hydrogen bonds, contacts, and hydrophobic burial and without bad contacts. Our model predicts the burial of CLIP residues Met-91 and Met-99 in the deep P1 and P9 anchor pockets and other detailed interactions, which we have compared with available data. The predicted pattern of I-A allele-specific effects on CLIP binding is very similar to that observed experimentally by alanine-scanning mutations of CLIP. Together, these results indicate that CLIP may bind in a single, general way across products of MHC class II alleles.

A general model of invariant chain association with class II major histocompatibility complex proteins

https://www.cell.com/structure/pdf/S1359-0278(96)00006-5.pdf

Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the Ala98→Val mutants of T4 lysozyme

Since the Rwandan genocide of 1994, an increase in scholarship on genocide and mass violence has developed over the past ten years, an interdisciplinary effort that has initiated a search for both a ‘usable past’ and at times a useful ‘theoretical past’. Against this backdrop, this article is concerned with the provisional re-emergence of Hannah Arendt's thought in African studies. It aims to explore the main facets of this under-recognised legacy to claim a contemporary place for her within the history of political thought on Africa and imperialism more generally. Divided into two parts, this essay first provides a summary of Arendt's engagement with imperial conditions in Africa, as found in her first major work The Origins of Totalitarianism (1951). Her influence is then traced in recent studies on South Africa and Rwanda, though not without critique. The insights and limitations of her interpretations rest on a distinction between ‘causes’ versus ‘conditions’, with her emphasis on the latter ...

‘Causes’ versus ‘Conditions’: Imperial Sovereignty, Postcolonial Violence and the recent Re-Emergence of Arendtian Political Thought in African Studies

This article examines the categorical problem that persons of ‘mixed-race’ background presented to British administrations in eastern, central and southern Africa during the late 1920s and 1930s. Tracing a discussion regarding the terms ‘native’ and ‘non-native’ from an obscure court case in Nyasaland (contemporary Malawi) in 1929, to the Colonial Office in London, to colonial governments in eastern, central and southern Africa, this article demonstrates a lack of consensus on how the term ‘native’ was to be defined, despite its ubiquitous use. This complication arrived at a particularly crucial period when indirect rule was being implemented throughout the continent. Debate centered largely around the issue of racial descent versus culture as the determining factor. The ultimate failure of British officials to arrive at a clear definition of the term ‘native’, one of the most fundamental terms in the colonial lexicon, is consequently suggestive of both the potential weaknesses of colonial state formation and the abstraction of colonial policy vis-a-vis local empirical conditions. Furthermore, this case study compels a rethinking of contemporary categories of analysis and their historical origins.

Christopher J. Lee

Papers

Making a World after Empire: The Bandung Moment and Its Political Afterlives

A general model of invariant chain association with class II major histocompatibility complex proteins

Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the Ala98→Val mutants of T4 lysozyme

‘Causes’ versus ‘Conditions’: Imperial Sovereignty, Postcolonial Violence and the recent Re-Emergence of Arendtian Political Thought in African Studies

The 'Native' Undefined: Colonial Categories, Anglo-African Status and the Politics of Kinship in British Central Africa, 1929-38