Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.

SARS-CoV-2 is the causative agent of COVID-19, the ongoing global pandemic. It has posed a worldwide challenge to human health as no effective treatment is currently available to combat the disease. Its severity has led to unprecedented collaborative initiatives for therapeutic solutions against COVID-19. Studies resorting to structure-based drug design for COVID-19 are plethoric and show good promise. Structural biology provides key insights into 3D structures, critical residues/mutations in SARS-CoV-2 proteins, implicated in infectivity, molecular recognition and susceptibility to a broad range of host species. The detailed understanding of viral proteins and their complexes with host receptors and candidate epitope/lead compounds is the key to developing a structure-guided therapeutic design. Since the discovery of SARS-CoV-2, several structures of its proteins have been determined experimentally at an unprecedented speed and deposited in the Protein Data Bank. Further, specialized structural bioinformatics tools and resources have been developed for theoretical models, data on protein dynamics from computer simulations, impact of variants/mutations and molecular therapeutics. Here, we provide an overview of ongoing efforts on developing structural bioinformatics tools and resources for COVID-19 research. We also discuss the impact of these resources and structure-based studies, to understand various aspects of SARS-CoV-2 infection and therapeutic development. These include (i) understanding differences between SARS-CoV-2 and SARS-CoV, leading to increased infectivity of SARS-CoV-2, (ii) deciphering key residues in the SARS-CoV-2 involved in receptor-antibody recognition, (iii) analysis of variants in host proteins that affect host susceptibility to infection and (iv) analyses facilitating structure-based drug and vaccine design against SARS-CoV-2

Narratives of spousal support for the careers of men in managerial posts

This article analyses the narratives of men managers to see how they perceive their wives' support in relation to their careers. Our aim is to focus on different forms of spousal support and explore how the support can evolve in the course of the men's careers. We are also interested in what kind of gender relations men produce when narrating their experiences of spousal support for their career. The research material comprises interviews with 29 managers who are fathers. In contrast to many previous studies, the results here suggest that spousal support is not a fixed or uncomplicated phenomenon but is constructed as various and flexible by men: negotiated , enriching and declining. The narrative analysis, in which we detected three different story‐lines — romance, ‘happily‐ever‐after’ and tragedy — shows that the most positive narratives in terms of life satisfaction and career success were those in which spousal support was constructed as negotiated and men were willing to be flexible and adaptable in their gender relations with their spouse. More attention to a father's work and family integration is needed in the field of management and organizations.peerReviewe