AIMC Journal:
bioRxiv

Showing 461 to 470 of 4935 articles

Physics-Informed Modeling of Biological Aging through DNA Methylation Entropy

bioRxiv Aug 20, 2026
Epigenetic clocks based on DNA methylation patterns are among the most accurate molecular correlates of chronological age, yet widely used clocks are predominantly empirical models with limited explicit characterization of the underlying methylation ...
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Dynamics-aware geometric learning predicts disease-associated molecular perturbations

bioRxiv Aug 20, 2026
Missense mutations and post-translational modifications (PTMs) are major molecular perturbations that reshape protein function but are traditionally studied independently. Current computational approaches largely rely on sequence conservation or stat...
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Makeshift: a lightweight software for accessing and analyzing NMR data and protein dynamics

bioRxiv Aug 20, 2026
Nuclear magnetic resonance (NMR) spectroscopy yields rich residue-level information on biomolecular dynamics and chemical environments, two frontiers for quantitative predictive methods in biochemistry. Decades of data are publicly archived in the Bi...
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Single-Molecule Proteomics via a Dynamic Translocase and Physics-Informed Machine Learning

bioRxiv Aug 20, 2026
Single-molecule protein sequencing promises to democratize clinical proteomics, but platforms retrofitting static DNA-sequencing nanopores face a fundamental biophysical bottleneck: they only measure one-dimensional excluded volume. Consequently, the...
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Mechanistic Dissection of Entropic Penalty upon Ligand Binding and Molecular Flexibility via Molecular Dynamics Simulations and Machine Learning

bioRxiv Aug 20, 2026
Molecular flexibility governs how molecules behave, reorganize, and respond to their environment. Although experiments measure molar entropy for small molecules and molecular dynamics (MD) simulations capture molecular motions, quantifying configurat...
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Supervised Learning of Phosphopeptide Sequence Constraints Enables Global Prediction of SH2 Domain Binding

bioRxiv Aug 19, 2026
Tyrosine kinase signaling for cell development and homeostasis in multicelluar organisms and a major biochemical contribution is by driving interactions between phosphorylated tyrosines (pY) and SH2 domain containing proteins. This assembly is so imp...
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Resolution-standardized evaluation of ligand atomic coordinates in crystallographic structures using machine learning

bioRxiv Aug 18, 2026
Accurate assessment of ligand coordinate-density consistency across different resolutions remains challenging in macromolecular crystallography. We introduce the atomic Box Correlation Coefficient (aBCC), an atom-level metric for evaluating the consi...
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A Generative Virtual Tissue Model Enables Computational Design of Therapeutic Perturbation Strategies

bioRxiv Aug 18, 2026
Computational design has transformed many fields of engineering, where simulators can explore millions of candidate design configurations before experimental development and testing. Therapeutic design in biomedicine has resisted computational design...
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Assessing the Reliability of LLM-Generated Phenotype-Genotype Associations Through External Validation

bioRxiv Aug 18, 2026
Background: Phenotype-genotype associations underpin precision medicine by enabling disease prevention, early diagnosis, risk stratification, therapeutic target discovery, and personalized treatment. However, the rapid growth of scientific evidence h...
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3D printing and deep learning enable holistic and dynamic analyses of tens of thousands of parasites infecting hundreds of genotypes

bioRxiv Aug 18, 2026
Host-parasite interactions are dynamic systems, where parasites usually outnumber hosts by one or more orders of magnitude. However, our understanding is often limited by the assessment of parts of the host, at arbitrary time points, and/or aggregate...
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