AIMC Journal:
bioRxiv

Showing 1481 to 1490 of 4956 articles

Sequence-based Drug-Target Binding Site Pre-training Enables Cryptic Pocket Detection and Improves Binding Affinity and Kinetics Prediction

bioRxiv May 18, 2026
Predicting protein-ligand binding characteristics, such as affinity and kinetics, is critical for accelerating drug discovery. However, many existing computational methods face key limitations, including insufficient integration of comprehensive data...
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NMR Spectroscopy for the Validation of AlphaFold2 Structures

bioRxiv May 18, 2026
The introduction of AlphaFold has fundamentally changed our ability to predict the structure of proteins from their primary sequence of amino acids. As machine learning (ML) and artificial intelligence (AI) based protein prediction continues to advan...
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Deep Learning Structural Ensembles as Proxies for Protein Flexibility

bioRxiv May 18, 2026
Protein dynamics are essential to biological function, yet understanding whether deep learning models contain information about these dynamics remains an open question. In this study, we quantitatively investigate the capacity of deep learning struct...
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Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope

bioRxiv May 18, 2026
HIV-1 buds from infected cells as immature virion particles with a scattered envelope glycoprotein (Env) distribution on their envelope. It then undergoes maturation, during which the viral protease cleaves the Gag polyprotein at multiple sites, lead...
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Transcript architecture predetermines m6A remodeling and sensory neuron vulnerability in chemotherapy-induced peripheral neuropathy

bioRxiv May 18, 2026
Whether individual transcripts carry intrinsic features that predetermine their response to external perturbations is unknown. Here we used nanopore direct RNA sequencing of male mouse dorsal root ganglia (DRG) to simultaneously profile N6-methyladen...
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FlexENN: A Graph Neural Network for Binding Energy Prediction of Globular and Intrinsically Disordered Proteins

bioRxiv May 18, 2026
Intrinsically disordered proteins (IDPs) drive a large fraction of cellular signaling, transcription and assembly through interfaces that lack a single defined geometry, making the prediction of their binding energies beyond the reach of methods cali...
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Learning from Drops: AI-Guided Integration of Liquid Biopsy Features in Cancer Studies

bioRxiv May 17, 2026
Cancer is a major global health issue with rising incidence and mortality. Early detection, tumor characterization, and disease surveillance are crucial for timely and effective treatment, ultimately reducing mortality rates. Liquid biopsy (LB) has e...
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Prepubertal ovariectomy alters dorsomedial striatum indirect pathway neuron excitability and explore/exploit balance in female mice

bioRxiv May 17, 2026
Decision-making circuits are modulated across life stages (e.g. juvenile, adolescent, or adult), as well as on the shorter timescale of reproductive cycles in females, to meet changing environmental and physiological demands. Ovarian hormone signalin...
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Evo 2 Predicts Cardiomyopathy-Associated Variants and Elucidates Their Underlying Mechanisms

bioRxiv May 17, 2026
Background: Although advances in next-generation sequencing have accelerated the identification of genetic variants in cardiomyopathy, interpreting variants of uncertain significance (VUS) remains a clinical challenge. Evo 2 is a high-resolution geno...
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Overweight status drives early tumor microenvironment reprogramming in pancreatic ductal adenocarcinoma: a cell-type-resolved Bayesian hierarchical modeling and interactome analysis

bioRxiv May 17, 2026
Background: Obesity significantly increases the risk of prognosis and clinical outcomes in pancreatic ductal adenocarcinoma (PDAC). While research on the interactions between obesity and the tumor microenvironment (TME) is mostly confined to a few in...
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