Explanipedia

Unpaid care, time taken off work and healthcare costs before and after partner bereavement among same-gender and different-gender partners: A national population-based study Open

Katherine Bristowe, Peter May, Alexandra Pitman, Jingjing Jiang, Liadh Timmins , et al. · 2025

Background: Recent research has demonstrated higher levels of psychological distress for bereaved same-gender partners compared to different-gender partners. Economic outcomes have not yet been examined. Aim: To examine whether there are d…

The AlphaFold Database Ages Open

Ifigenia Tsitsa, Anja Conev, Alessia David, Suhail A. Islam, Michael J.E. Sternberg · 2025

The AlphaFold database provides 200M protein structures predicted by AlphaFold2 and released in 2022 from sequences in UniProt in April 2021. However, of the 20,504 full-length human structures in the AlphaFold database, 631 entries confli…

Phyre2.2: A Community Resource for Template-based Protein Structure Prediction Open

Harold R. Powell, Suhail A. Islam, Alessia David, Michael J.E. Sternberg · 2025

Template-based modelling, also known as homology modelling, is a powerful approach to predict the structure of a protein from its amino acid sequence. The approach requires one to identify a sequence similarity between the query sequence a…

Between loss and restoration: The role of liminality in advancing theories of grief and bereavement Open

Katherine Bristowe, Liadh Timmins, Alexandra Pitman, Debbie Braybrook, Steve Marshall , et al. · 2024

Phyre2.2: A Community Resource for Template-Based Protein Structure Prediction Open

Harold R. Powell, Suhail A. Islam, Alessia David, Michael J.E. Sternberg · 2024

Missense3D-TM: Predicting the Effect of Missense Variants in Helical Transmembrane Protein Regions Using 3D Protein Structures Open

Gordon Hanna, Tarun Khanna, Suhail A. Islam, Alessia David, Michael J.E. Sternberg · 2023

Variant effect predictors assess if a substitution is pathogenic or benign. Most predictors, including those that are structure-based, are designed for globular proteins in aqueous environments and do not consider that the variant residue …

Protein structure-based evaluation of missense variants: Resources, challenges and future directions Open

Alessia David, Michael J.E. Sternberg · 2023

We provide an overview of the methods that can be used for protein structure-based evaluation of missense variants. The algorithms can be broadly divided into those that calculate the difference in free energy (ΔΔG) between the wild type a…

Missense3D-PPI: A Web Resource to Predict the Impact of Missense Variants at Protein Interfaces Using 3D Structural Data Open

Cecilia Pennica, Gordon Hanna, Suhail A. Islam, Michael J.E. Sternberg, Alessia David · 2023

In 2019, we released Missense3D which identifies stereochemical features that are disrupted by a missense variant, such as introducing a buried charge. Missense3D analyses the effect of a missense variant on a single structure and thus may…

A new web resource to predict the impact of missense variants at protein interfaces using 3D structural data: Missense3D-PPI Open

Cecilia Pennica, Gordon Hanna, Suhail A. Islam, Michael J.E. Sternberg, Alessia David · 2023

In 2019, we released Missense3D which identifies stereochemical features that are disrupted by a missense variant, such as introducing a buried charge. Missense3D analyses the effect of a missense variant on a single structure and thus may…

LGBT+ partner bereavement and appraisal of the Acceptance-Disclosure Model of LGBT+ bereavement: A qualitative interview study Open

Katherine Bristowe, Liadh Timmins, Debbie Braybrook, Steve Marshall, Alexandra Pitman , et al. · 2022

Background: Support from social networks is vital after the death of a partner. Lesbian, gay, bisexual and/or transgender (LGBT+) people can face disenfranchisement and isolation in bereavement. The Acceptance-Disclosure Model (of LGBT+ be…

Does the impact of bereavement vary between same and different gender partnerships? A representative national, cross-sectional study Open

Liadh Timmins, Alexandra Pitman, Michael J.E. Sternberg, Wei Gao, Katherine Johnson , et al. · 2022

Background Data suggest poorer bereavement outcomes for lesbian, gay and bisexual people, but this has not been estimated in population-based research. This study compared bereavement outcomes for partners of same-gender and different-gend…

GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes Open

S. B. Malladi, Harold R. Powell, Alessia David, Suhail A. Islam, Matthew M. Copeland , et al. · 2022

Bioblox 2.5D -- Developing an Educational Game Based on Protein Docking Open

Frédéric Fol Leymarie, William Latham, Guido Salimbeni, Suhail A. Islam, Christopher R. Reynolds , et al. · 2022

We present the development process of Bioblox2-5D, an educational biology game aimed at teenagers. The game content refers to protein docking and aims to improve learning about molecular shape complexity, the roles of charges in molecular …

3DLigandSite: structure-based prediction of protein–ligand binding sites Open

Jake E McGreig, Hannah Uri, Magdalena Antczak, Michael J.E. Sternberg, Martin Michaelis , et al. · 2022

3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites…

A common TMPRSS2 variant has a protective effect against severe COVID-19 Open

Alessia David, Nick Parkinson, Thomas P. Peacock, Erola Pairo‐Castineira, Tarun Khanna , et al. · 2022

The SARS-CoV-2 infection in Thailand: analysis of spike variants complemented by protein structure insights Open

Sirawit Ittisoponpisan, Shalip Yahangkiakan, Michael J.E. Sternberg, Alessia David · 2022

Thailand was the first country outside China to officially report COVID-19 cases. Despite the strict regulations for international arrivals, up until February 2021, Thailand had been hit by two major outbreaks. With a large number of SARS-…

Longitudinal Outcomes of Gender Identity in Children (LOGIC): study protocol for a retrospective analysis of the characteristics and outcomes of children referred to specialist gender services in the UK and the Netherlands Open

Eilis Kennedy, Chloe Lane, Hannah Stynes, Veronica Ranieri, Lauren Spinner , et al. · 2021

Introduction Specialist gender services for children and young people (CYP) worldwide have experienced a significant increase in referrals in recent years. As rates of referrals increase, it is important to understand the characteristics a…

The AlphaFold Database of Protein Structures: A Biologist’s Guide Open

Alessia David, Suhail A. Islam, Evgeny Tankhilevich, Michael J.E. Sternberg · 2021

AlphaFold, the deep learning algorithm developed by DeepMind, recently released the three-dimensional models of the whole human proteome to the scientific community. Here we discuss the advantages, limitations and the still unsolved challe…

PDBe-KB: collaboratively defining the biological context of structural data Open

Mihály Váradi, Stephen Anyango, David Armstrong, John M. Berrisford, Preeti Choudhary , et al. · 2021

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Pr…

A common TMPRSS2 variant protects against severe COVID-19 Open

Alessia David, Nick Parkinson, Thomas P. Peacock, Erola Pairo‐Castineira, Tarun Khanna , et al. · 2021

Summary Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing cond…

The mental health of lesbian, gay, and bisexual adults compared with heterosexual adults: results of two nationally representative English household probability samples Open

Alexandra Pitman, Louise Marston, Gemma Lewis, Joanna Semlyen, Sally McManus , et al. · 2021

Background Evidence on inequalities in mental health in lesbian, gay, and bisexual people arises primarily from non-random samples. Aims To use a probability sample to study change in mental health inequalities between two survey points, 7…

Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants Open

Tarun Khanna, Gordon Hanna, Michael J.E. Sternberg, Alessia David · 2021

A Common TMPRSS2 Variant Protects Against Severe COVID-19 Open

Alessia David, Nick Parkinson, Thomas P. Peacock, Erola Pairo‐Castineira, Tarun Khanna , et al. · 2021

Annotation and curation of human genomic variations: an ELIXIR Implementation Study Open

Alessia David, Valérie Barbié, Marcella Attimonelli, Roberto Preste, Enni Makkonen , et al. · 2020

Background: ELIXIR is an intergovernmental organization, primarily based around European countries, established to host life science resources, including databases, software tools, training material and cloud storage for the scientific com…

LGR4 deficiency results in delayed puberty through impaired Wnt/β-catenin signaling Open

Alessandra Mancini, Sasha Howard, Federica Marelli, Claudia Cabrera, Michael R. Barnes , et al. · 2020

The initiation of puberty is driven by an upsurge in hypothalamic gonadotropin-releasing hormone (GnRH) secretion. In turn, GnRH secretion upsurge depends on the development of a complex GnRH neuroendocrine network during embryonic life. A…

Structure, function and variants analysis of the androgen-regulatedTMPRSS2, a drug target candidate for COVID-19 infection Open

Alessia David, Tarun Khanna, Melina Beykou, Gordon Hanna, Michael J.E. Sternberg · 2020

SARS-CoV-2 is a novel virus causing mainly respiratory, but also gastrointestinal symptoms. Elucidating the molecular processes underlying SARS-CoV-2 infection, and how the genetic background of an individual is responsible for the variabi…

Issue Information ‐ Forthcoming Open

Christina Bergonzo, Kunal Dharmadhikari, E Samuels, Makenzie Christensen, Jennifer Tullman , et al. · 2020

A polygenic biomarker to identify patients with severe hypercholesterolemia of polygenic origin Open

Luis G. Leal, Clive Hoggart, Marjo-Riitta Järvelin, Karl‐Heinz Herzig, Michael J.E. Sternberg , et al. · 2020

Background Severe hypercholesterolemia (HC, LDL‐C > 4.9 mmol/L) affects over 30 million people worldwide. In this study, we validated a new polygenic risk score (PRS) for LDL‐C. Methods Summary statistics from the Global Lipid Genome Conso…

Issue Information ‐ Forthcoming Open

Ren Kong, Ranran Liu, Ximing Xu, Dawei Zhang, Xiaoshuang Xu , et al. · 2020

Application of docking methodologies to modeled proteins Open

Amar Singh, Taras Dauzhenka, Petras J. Kundrotas, Michael J.E. Sternberg, Ilya A. Vakser · 2020

Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles …

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