Related papers: Power and limitations of electrophoretic separatio…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
Many complex systems can be represented as networks composed by distinct layers, interacting and depending on each others. For example, in biology, a good description of the full protein-protein interactome requires, for some organisms, up…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
In post genomic era with the advent of new technologies a huge amount of complex molecular data are generated with high throughput. The management of this biological data is definitely a challenging task due to complexity and heterogeneity…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
``Seeding'' is the addition of preformed fibrils to a solution of monomeric protein to accelerate its aggregation into new fibrils. It is a versatile and widely-used tool for scientists studying protein aggregation kinetics, as it enables…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
We report an alternative method for electrophoretic separation of large DNAs using steric confinement between solid walls, without gel or obstacles. The change of electrophoretic mobility vs confinement thickness is investigated using…
Tautomers are ubiquitous throughout chemistry, and typically considered inseparable in solution. Yet (bio)chemical activity is highly tautomer specific, with common examples being the amino and nucleic acids. While tautomers exist in an…
The techniques of principal and independent component analysis are applied to images of ultracold atoms. As an illustrative example, we present the use of these model-independent methods to rapidly determine the differential phase of a BEC…
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…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
This paper presents an approach to the evaluation and validation of mass spectrometry data for construction of an `early warning' diagnostic procedure. We describe implementation of a designed experiment and place emphasis on the consistent…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
Heteropolymer gels can be engineered to release specific molecules into or absorb molecules from a surrounding solution. This remarkable ability is the basis for developing gel applications in extensive areas such as drug delivery, waste…