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The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Estimating $T_2$ relaxation time distributions from multi-echo $T_2$-weighted MRI ($T_2W$) data can provide valuable biomarkers for assessing inflammation, demyelination, edema, and cartilage composition in various pathologies, including…
De novo peptide sequencing from mass spectrometry data is an important method for protein identification. Recently, various deep learning approaches were applied for de novo peptide sequencing and DeepNovoV2 is one of the represetative…
Understanding the spatial architecture of the tumor microenvironment (TME) is critical to advance precision oncology. We present ProteinPNet, a novel framework based on prototypical part networks that discovers TME motifs from spatial…
Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Over the last years, the SWATH data-independent acquisition protocol (Sequential Window acquisition of All THeoretical mass spectra) has become a cornerstone for the worldwide proteomics community. In this approach, a high-resolution…
Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of…
The unbounded permutations of biological molecules, including proteins and their constituent peptides, presents a dilemma in identifying the components of complex biosamples. Sequence search algorithms used to identify peptide spectra can…
Recently, many software tools have been developed to perform quantification in LC-MS analyses. However, most of them are specific to either a quantification strategy (e.g. label-free or isotopic labelling) or a mass-spectrometry system…
Metabolite structure identification has become the major bottleneck of the mass spectrometry based metabolomics research. Till now, number of mass spectra databases and search algorithms have been developed to address this issue. However,…
Plastid targeted proteins of diatoms and related algae can be predicted with high sensitivity and specificity using the ASAFind method published in 2015. ASAFind predictions rely on SignalP predictions of endoplasmic reticulum (ER)…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
Prostate cancer is the most abundant cancer in men, with over 200,000 expected new cases and around 28,000 deaths in 2012 in the US alone. In this study, the segmentation results for the prostate central gland (PCG) in MR scans are…
Intrinsically disordered regions of proteins play a crucial role in cell signaling and drug discovery. However, their high structural flexibility makes accurate residue-level prediction challenging. Existing methods often rely on…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…