Related papers: Sampling the proteome by emerging single-molecule …
At the intersection of the rapidly growing biological data landscape and advancements in Natural Language Processing (NLP), protein language models (PLMs) have emerged as a transformative force in modern research. These models have achieved…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Many {\it ribosomes} simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here {\it we develop a ``unified'' theoretical model} that not only…
Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In…
Mass spectrometry-based metabolomic analysis depends upon the identification of spectral peaks by their mass and retention time. Statistical analysis that follows the identification currently relies on one main peak of each compound.…
Simplified Molecular Input Line Entry System (SMILES) is a single line text representation of a unique molecule. One molecule can however have multiple SMILES strings, which is a reason that canonical SMILES have been defined, which ensures…
Molecular optimization is a fundamental goal in the chemical sciences and is of central interest to drug and material design. In recent years, significant progress has been made in solving challenging problems across various aspects of…
The advent of single molecule microscopy has revolutionized biological investigations by providing a powerful tool for the study of intercellular and intracellular trafficking processes of protein molecules which was not available before…
While protein language models (pLMs) have transformed biological research, the scaling laws governing their improvement remain underexplored. By adapting methodologies from NLP scaling laws, we investigated the optimal ratio between model…
Here, we discuss a collection of cutting-edge techniques and applications in use today by some of the leading experts in the field of correlative approaches in single-molecule biophysics. A key difference in emphasis, compared with…
Diffusion coefficient measurements are important for many biological and material investigations, such as particle dynamics, kinetics, and size determinations. Amongst current measurement methods, single particle tracking (SPT) offers the…
Recent advancements in large language models (LLMs) have demonstrated impressive performance in molecular generation, which offers potential to accelerate drug discovery. However, the current LLMs overlook a critical requirement for drug…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently,…
With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…
The common techniques to study protein-protein proximity in vivo are not well-adapted to the capabilities and the expertise of a standard proteomics laboratory, typically based on the use of mass spectrometry. With the aim of closing this…