AIMC Topic: Protein Binding
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Human protein interaction networks of ancestral and variant SARS-CoV-2 in organ-specific cells and bodily fluids.
Nature communications
Jul 1, 2025
Understanding SARS-CoV-2 human protein-protein interactions (PPIs) and the host response to infection is essential for developing effective COVID-19 antivirals. However, how the ancestral virus and its variants remodel virus-host protein assemblies i...
Charting γ-secretase substrates by explainable AI.
Nature communications
Jul 1, 2025
Proteases recognize substrates by decoding sequence information-an essential cellular process elusive when recognition motifs are absent. Here, we unravel this problem for γ-secretase, an intramembrane-cleaving protease associated with Alzheimer's di...
Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA-A0201.
PloS one
Jun 27, 2025
Class Ι major histocompatibility complexes (MHC-Ι), encoded by the highly polymorphic HLA-A, HLA-B, and HLA-C genes in humans, are expressed on all nucleated cells. Both self and foreign proteins are processed to peptides of 8-10 amino acids, loaded ...
In-silico study of approved drugs as potential inhibitors against 3CLpro and other viral proteins of CoVID-19.
PloS one
Jun 25, 2025
The global pandemic, due to the emergence of COVID-19, has created a public health crisis. It has a huge morbidity rate that was never comprehended in the recent decades. Despite numerous efforts, potent antiviral drugs are lacking. Repurposing of dr...
generation of peptide binders with desired properties by deep generative models reinforced through enrichment of focused sets for iterative fine-tuning.
Chemical communications (Cambridge, England)
Jun 24, 2025
Recurrent neural networks underwent reinforcement procedures for generation of peptide binders with desired properties. Docking and scoring of peptides from these models allowed enrichment of focused sets with validated sequences for iterative fine-...
Divergence in a eukaryotic transcription factor's co-TF dependence involves multiple intrinsically disordered regions.
Nature communications
Jun 18, 2025
Combinatorial control by transcription factors (TFs) is central to eukaryotic gene regulation, yet its mechanism, evolution, and regulatory impact are not well understood. Here we use natural variation in the yeast phosphate starvation (PHO) response...
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction.
Journal of chemical information and modeling
Jun 2, 2025
The black-box nature of deep learning has increasingly drawn attention to the reliability and uncertainty of predictive models. Currently, several uncertainty quantification (UQ) methods have been proposed and successfully applied in the fields of mo...
Molecular insights into the unique activation and allosteric modulation mechanisms of the human mas-related G-protein-coupled receptor X1.
International journal of biological macromolecules
May 30, 2025
MRGPRX1 plays dual roles in mediating nociception and pruritus, making it a promising target for alleviating itch and inhibiting pain. However, the mechanisms underlying MRGPRX1 activation and allosteric modulation remain poorly understood, posing si...
AI, docking, and molecular dynamics to track the binding of structural peptides to different keratin models.
International journal of biological macromolecules
May 30, 2025
The present work shows a computational approach to assess the interactions of different nature-inspired peptides with hair keratin models. An updated keratin model was validated, and comparisons with previous models were traced, thereby highlighting ...
Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.
eLife
May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
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