Related papers: XLMOD: Cross-linking and chromatography derivatiza…
Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination,…
Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats,…
Recent development of high-resolution mass spectrometry (MS) instruments enables chemical cross-linking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or…
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins…
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…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
Biological processes rely on finely tuned homo- and heteromeric interactions between (biomacro)molecules. The strength of an interaction, typically given by the dissociation constant (KD), plays a crucial role in basic research and must be…
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…
Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures.…
Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical…
The identification and property prediction of chemical molecules is of central importance in the advancement of drug discovery and material science, where the tandem mass spectrometry technology gives valuable fragmentation cues in the form…
Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel…
Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…
Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic,…
Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of…
Protein circular permutations are crucial for understanding protein evolution and functionality. Traditional detection methods, sequence-based or structure-based, struggle with accuracy and computational efficiency, the latter also limited…
Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…