Related papers: Power and limitations of electrophoretic separatio…
Identification of nearly all proteins in a system using data-dependent acquisition (DDA) mass spectrometry has become routine for simple organisms, such as bacteria and yeast. Still, quantification of the identified proteins may be a…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Biomolecular condensates, physically underpinned to a significant extent by liquid-liquid phase separation (LLPS), are now widely recognized by numerous experimental studies to be of fundamental biological, biomedical, and biophysical…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Porous gels -- gels with solvent-filled pores that are much larger than their mesh size -- are widely used in engineering and biomedical applications due to their tunable mechanics, high water content, and selective permeability. Among…
Phenomenological screening of small molecule libraries for anticancer activity yields potentially interesting candidate molecules, with a bottleneck in the determination of drug targets and the mechanism of anticancer action. A novel…
Phase separation of various materials has been studied for one and a half centuries. In the last two decades, phase separation of proteins and nucleic acids has received enormous attention, due its relevance to cellular functions. However,…
Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion…
Proteinoids -- thermal proteins -- are produced by heating amino acids to their melting point and initiation of polymerisation to produce polymeric chains. Proteinoids swell in aqueous solution into hollow microspheres. The proteinoid…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
The mechanism by which silver staining of proteins in polyacrylamide gels interferes with mass spectrometry of peptides produced by proteolysis has been investigated. It was demonstrated that this interference increases with time between…
Data mining techniques have been used by researchers for analyzing protein sequences. In protein analysis, especially in protein sequence classification, selection of feature is most important. Popular protein sequence classification…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
Electron energy loss spectroscopy is consolidating as a powerful tool to explore electronic (as well as vibrational) excitations of matter, including molecules. Performed in a scanning transmission electron microscope, this technique is…
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…
Protein corona formation and nanoparticle aggregation have been heavily discussed over the last years since the lack of fine-mapping of these two combined effects has hindered the targeted delivery evolution and the personalized…