Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.

Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (AF), this study computationally examines the entire UniProt database to create a robust dataset of knotted and unknotted proteins. Utilizing this dataset, we develop a machine learning (ML) model capable of accurately predicting the presence of knots in protein structures solely from their amino acid sequences.

AlphaFold predicts novel human proteins with knots.

The fact that proteins can have their chain formed in a knot is known for almost 30 years. However, as they are not common, only a fraction of such proteins is available in the Protein Data Bank. It was not possible to assess their importance and versatility up until now because we did not have access to the whole proteome of an organism, let alone a human one.

New lung mass in a patient with granulomatosis with polyangiitis.

Granulomatosis with polyangiitis (GPA) is a potentially lethal ANCA-associated small-vessel vasculitis characterized by a typical triad of upper respiratory tract, lung, and kidney involvement. Lung involvement in GPA occurs in 25-80% of cases. The most common radiographic and computed tomography (CT) abnormalities of pulmonary GPA are lung nodules and masses, very often multiple and with cavitation.

Changed phagocytic activity and pattern of Fcγ and complement receptors on blood monocytes in sarcoidosis.

We have recently revealed that mycobacterial heat shock proteins (Mtb-hsp), involved in forming of immune complexes (CIs), can induce immune response in sarcoidosis (SA). The complexemia may result from inappropriate phagocytosis and clearance of CIs by monocytes with following persistent antigenemia and granuloma formation. Because an aberrant expression of receptors for Fc fragment of immunoglobulin G (FcγR) and complement receptors (CR) on monocytes can be involved in this process, we have evaluated the expression of FcγRI (CD64), FcγRII (CD32), FcγRIII (CD16) and CR1 (CD35), CR3 (CD11b), CR4 (CD11c) receptors on blood CD14(+) monocytes and its phagocytic activity in 24 patients with SA and 20 healthy volunteers using flow cytometry.

Ideal amino acid exchange forms for approximating substitution matrices.

We have analyzed 29 published substitution matrices (SMs) and five statistical protein contact potentials (CPs) for comparison. We find that popular, 'classical' SMs obtained mainly from sequence alignments of globular proteins are mostly correlated by at least a value of 0.9.

Library of local descriptors models the core of proteins accurately.

In this article, we present a novel approach to describing proteins based on multifragment structure motifs called local descriptors. We collect structurally similar descriptors in groups to construct a compact library of groups of descriptors. To demonstrate its feasibility for a wide spectrum of applications, ranging from structure comparison and analysis to structure prediction, it is critical to show the ability of groups from our library to reproduce proteins accurately.

A new approach to the assessment of the quality of predictions of transcription factor binding sites.

In this paper, we describe a novel method called Secondary Verification which assesses the quality of predictions of transcription factor binding sites. This method incorporates a distribution of prediction scores over positive examples (i.e.