Plasma proteome fingerprint in kidney diseases.

Introduction: Kidney diseases pose a serious healthcare problem because of their high prevalence, worsening of patients' quality of life, and high mortality. Patients with kidney diseases are often asymptomatic until disease progression starts. Expensive renal replacement therapy options, such as dialysis or kidney transplant, are required for end-stage kidney disease.

PSSKB: A Web Application to Study Protein Structures.

The proteins expressed during the cell cycle determine cell function and ensure signaling pathway activation in response to environmental influences. Developments in structural biology, biophysics, and bioinformatics provide information on the structure and function of particular proteins including that on the structural changes in proteins due to post-translational modification (PTM) and amino acid substitutions (AAS), which is essential for understanding protein function and life cycle. These are PTMs and AASs that often modulate the function and alter the stability and localization of a protein in a cell.

Sample Preparation for Metabolomic Analysis in Exercise Physiology.

Metabolomics investigates final and intermediate metabolic products in cells. Assessment of the human metabolome relies principally on the analysis of blood, urine, saliva, sweat, and feces. Tissue biopsy is employed less frequently.

PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models.

The primary objective of analyzing the data obtained in a mass spectrometry-based proteomic experiment is peptide and protein identification, or correct assignment of the tandem mass spectrum to one amino acid sequence. Comparison of empirical fragment spectra with the theoretical predicted one or matching with the collected spectra library are commonly accepted strategies of proteins identification and defining of their amino acid sequences. Although these approaches are widely used and are appreciably efficient for the well-characterized model organisms or measured proteins, they cannot detect novel peptide sequences that have not been previously annotated or are rare.

Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications.

Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications.

PSSNet-An Accurate Super-Secondary Structure for Protein Segmentation.

A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation.

Current Approaches in Supersecondary Structures Investigation.

Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research.