Introduction to Protein Structure Prediction

This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated

Preface to Introduction to Structural Bioinformatics

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics

Power in organizational life:An investigation of how stable and unstable power affect important organizational and leadership outcomes

Power is a fundamental feature of organizational life. Considering the important role of power in organizations, it seems crucial to understand how power affects its beholders. This dissertation examines power in an organizational context, and by doing so, contributes to the understanding of power in meaningful ways. First, this dissertation moves towards a more dynamic view of power by illustrating that the (in)stability of power hierarchies should be considered in order to fully understand the consequences of power in organizations. Second, this dissertation moves towards a more nuanced view of power and unethical behavior by showing that power is not always a corrupting force. Overall, this dissertation aims to shine more light on one of the most fundamental constructs in organizations: power

Strategies for protein structure model generation

This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling techniques are treated, and how resulting structural models may be selected and refined. We give a concrete flowchart for how to de- cide which modelling strategy is best suited in particular circumstances, and which steps need to be taken in each strategy. Notably, the ability to locate a suitable structural template by homology or fold recognition is crucial; without this models will be of low quality at best. With a template avail- able, the quality of the query-template alignment crucially determines the model quality. We also discuss how other, courser, experimental data may be incorporated in the modelling process to alleviate the problem of missing template structures. Finally, we discuss measures to predict the quality of models generated

Managerial stereotypes over time:the rise of feminine leadership

PurposeA key obstacle to women’s advancement to managerial roles and leadership positions is the stereotype of the “good” manager, which is characterized by masculine traits. Although this gendered managerial stereotype has been very persistent over the past decades, Powell et al. (2021) recently showed that business students in the USA reported a decreased preference for masculine leadership traits and an increased preference for feminine leadership traits, resulting in a so-called “androgynous” manager profile that contains both masculine and feminine characteristics. This study aims to replicate Powell et al.’s (2021) findings among an older sample of working adults in The Netherlands.Design/methodology/approachThe present study tests for changes in the managerial stereotype in a sample of 5,542 Dutch employees across 2005, 2010 and 2020.FindingsIn line with Powell et al. (2021), the results confirm employees’ decreased preference for masculine and increased preference for feminine leadership traits in 2020 compared to 2005. Nevertheless, Dutch employees still favored masculine over feminine leadership traits in 2020, contrary to the findings by Powell et al. (2021).Practical implicationsThese observed changes in the managerial stereotype could prove to be an important step forward for women’s advancement to management and leadership positions.Originality/valueWith the present study, the authors demonstrate cross-cultural generalizability and conclude that the stereotype of a “good manager” is not only changing among US business students but also among working adults in The Netherlands. Overall, this study strengthens the observation that the stereotype of a “good manager” is becoming less gendered

Antecedents of leaders' power sharing:The roles of power instability and distrust

Although previous research has identified various beneficial consequences of power sharing, less research has examined antecedents of leaders’ power sharing. To address this gap, across five studies, the present research identifies important social and psychological barriers to leaders’ power sharing. Studies 1a, 1b, and 2 demonstrate that the instability of a leader’s power position undermines his or her power sharing. Study 3 then demonstrates that distrust acts as a key psychological mechanism that can explain this relationship. Then, in Study 4, we distinguish between two dimensions of distrust and examine the moderating role of subordinates’ seniority. We show that subordinates’ seniority moderates the indirect association between power instability and power sharing, via benevolence and ability distrust, such that this indirect relationship is more pronounced for relatively senior (compared to junior) subordinates. Overall, our findings provide valuable insights into when, why, and with whom leaders are more or less willing to share their power

Rival or comrade? A systematic review and conceptual framework of when and why the powerful act prosocially or antisocially towards each other

We present a systematic review of the literature on power and its interpersonal consequences. Our review, comprising 339 studies published in 145 research articles, shows that this line of research has primarily examined how powerholders attend to and act towards powerless individuals, or others in general. We therefore know surprisingly little about how powerholders attend to and act towards other powerholders. To address this issue, we present a conceptual framework that outlines how an actor's power interacts with a target's power to influence prosocial and antisocial beliefs, attitudes, and behaviors. We identify two routes in the literature detailing how powerholders respond to one another. First, building on rivalry literature, we present a competitive route suggesting that powerholders rival each other and engage in conflict. Second, building on social identity and social dominance literature, we present a harmonious route suggesting that powerful peers will show compassion and care for each other. Finally, we bring forth suggestions for how future research could test these two perspectives, by presenting moderators that determine when each of these two routes is activated. In doing so, we offer important implications for the power literature and open a new line of inquiry for future research

Data Resources for Structural Bioinformatics

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. Structural bioinformatics involves a variety of computational methods, all of which require input data. Typical inputs include protein structures and sequences, which are usually retrieved from a public or private database. This chapter introduces several key resources that make such data available, as well as a handful of tools that derive additional information from experimentally determined or computationally predicted protein structures and sequences.Comment: editorial responsability: Sanne Abeln, K. Anton Feenstra, Halima Mouhib. This chapter is part of the book "Introduction to Protein Structural Bioinformatics". The Preface arXiv:1801.09442 contains links to all the (published) chapters. The update adds available arxiv hyperlinks for the chapter