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<h4>Motivation</h4>Accurate prediction of HIV drug resistance from viral sequences is critical for optimizing antiretroviral therapy. Traditional machine-learning approaches using binary mutation encoding achieve strong accuracy but may fail to capture epistatic interactions and structural features …
Read PDF<h4>Background and aims</h4>Familial Mediterranean Fever (FMF) is a monogenic autoinflammatory disease caused by mutations in the <i>MEFV</i> gene, resulting in recurrent inflammatory episodes and a risk of developing amyloidosis. Although its pathophysiology is well described, …
Read PDF<h4>Summary</h4>The protonation propensity of ionizable residues in proteins can change in response to changes in the local residue environment. The link between protein dynamics and pKa is particularly important in pH regulation of protein structure …
Read PDF<h4>Motivation</h4>Advances in tumor sequencing enable routine detection of dozens to hundreds of somatic alterations per patient, yet only a minority can be linked to established therapeutic evidence. Curated resources such as OncoKB provide high-quality variant-drug …
Read PDF<h4>Motivation</h4>Protein structure generative models have seen a recent surge of interest, but meaningfully evaluating them computationally is an active area of research. While current metrics have driven useful progress, they do not capture how well …
Read PDF<h4>Motivation</h4>Microbial biotransformation plays a central role in the environmental degradation of chemical contaminants, driven by the catalytic activities of diverse enzymes. However, linking specific enzymes to contaminant removal and predicting associated transformation products (TPs) under …
Read PDF<h4>Motivation</h4>Rational molecule generation that balances binding affinity with favorable physicochemical properties remains a formidable challenge in structure-based drug design. The number of functional groups is a key determinant, as over-functionalization compromises physicochemical properties, whereas under-functionalization …
Read PDF<h4>Motivation</h4>RNA-protein interactions play essential roles in every living organism, with RNA transcription, processing, and translation being just a few examples. Therefore, determining the set of RNAs that are bound by individual RNA-binding proteins, as well …
Read PDF<h4>Motivation</h4>Although deep learning has significantly advanced the field of protein function prediction, current approaches are limited by their reliance on a narrow set of modalities. Specifically, they primarily rely on sequence patterns and treat protein …
Read PDFSNP microarrays provide a cost-effective genotyping method used in various scientific disciplines. Sample costs vary from tens to hundreds of dollars, storage costs are comparatively reasonable, and analysis methods easily scale to large sample sizes. …
Read PDFOveruse of antimicrobial drugs is known to cause an increase in bacterial resistance among surviving pathogens, reducing the effectiveness of future treatments. Publicly available sequencing collections, such as the National Center for Biotechnology Information Sequence …
Read PDF<h4>Motivation</h4>Proteomics has experienced substantial growth in methods and data analysis approaches, with the development of new data-dependent (DDA) and data-independent acquisition (DIA) workflow and several search engine algorithms and software packages. Each of these workflows …
Read PDF<h4>Motivation</h4>Traditional drug discovery methods are costly and inefficient, while existing deep learning approaches remain limited by task specificity and practical applicability. Accurately modeling protein-molecule interactions is critical for advancing virtual screening, docking, and drug design.<h4>Results</h4>We …
Read PDFBioinformatics and artificial intelligence (AI) have become a new direction in dentistry, enabling predictive, precision-focused surgical care. In oral surgery and dental implant procedures, postoperative healing outcomes are inconsistent across most cases. These outcomes are …
Read PDFThis study evaluated the structural, electronic, pharmacokinetic, and receptor-binding properties of three bisphosphonate derivatives, alendronate, risedronate, and zoledronate, to investigate their therapeutic relevance in osteoporosis and breast cancer. Density Functional Theory (DFT) calculations at the …
Read PDF<h4>Objectives</h4>Soft tissue sarcomas (STSs) are rare, heterogeneous cancers with over 70 subtypes, often diagnosed late due to diagnostic complexity, leading to poor outcomes. We aimed to identify and validate novel transcriptomic biomarkers for the diagnosis …
Read PDF<h4>Motivation</h4>Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and human annotations, struggle …
Read PDFOrthology provides a powerful framework for investigating the evolutionary history of biological systems, as genes within the same orthologous group typically share a common ancestry. By tracing their distribution across species, it is possible to …
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