Related papers: Best practices for the manual curation of Intrinsi…

In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…

Intrinsically disordered regions (IDRs) play central roles in cellular function, yet remain poorly evaluated by existing protein structure prediction benchmarks. Current evaluations largely focus on well-folded domains, overlooking three…

Intrinsically Disordered Proteins (IDPs) constitute a large and structure-less class of proteins with significant functions. The existence of IDPs challenges the conventional notion that the biological functions of proteins rely on their…

Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…

Intrinsically disordered regions (IDRs) account for one-third of the human proteome and play essential biological roles. However, predicting the functions of IDRs remains a major challenge due to their lack of stable structures, rapid…

The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…

Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs/IDRs) are defined by diverse and dynamical structural…

Protein structure prediction has advanced significantly with the introduction of AlphaFold3, a diffusion-based model capable of predicting complex biomolecular interactions across proteins, nucleic acids, small molecules, and ions. While…

Intrinsically disordered protein regions (IDRs) are found across all domains of life and are characterized by a lack of stable 3D structure. Nevertheless, IDRs play critical roles in the most tightly regulated cellular processes, including…

AI systems represented by AlphaFold are rapidly expanding the scale of protein structure modelling data, and the MineProt project provides an effective solution for custom curation of these novel high-throughput data. It enables researchers…

Intrinsically disordered proteins are fascinating the community of protein science since the last decade, at least. There is a well-established line of research that intends to reveal the crucial role played by intrinsically disordered…

In this paper we propose a straightforward operational definition of variants of disordered proteins, taking the human proteome as a case study. The focus is on a distinction between mostly unstructured proteins and proteins which contain…

Data curation is a field with origins in librarianship and archives, whose scholarship and thinking on data issues go back centuries, if not millennia. The field of machine learning is increasingly observing the importance of data curation…

Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…

Deep neural networks (DNNs) are increasingly being deployed in high-stakes applications, from self-driving cars to biometric authentication. However, their unpredictable and unreliable behaviors in real-world settings require new approaches…

We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein…

Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires…

The extraction of pharmacological knowledge from regulatory documents has become a key focus in biomedical natural language processing, with applications ranging from adverse event monitoring to AI-assisted clinical decision support.…

Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…

Data curation is the process of making a dataset fit-for-use and archiveable. It is critical to data-intensive science because it makes complex data pipelines possible, makes studies reproducible, and makes data (re)usable. Yet the…