DynGeo-Pheno is presented, a unified geometric deep learning framework that integrates protein language model representations with anisotropic network model–derived dynamics to jointly capture evolutionary, structural, and biophysical information and establishes a unified framework for interpretable AI predictions and mechanistic understanding of how genetic and regulatory perturbations may shape protein function.
AlloPool is presented, a graph neural network (GNN)-based framework that interprets molecular dynamics simulations by iteratively pruning residue–residue interactions to uncover minimal, time-resolved interaction networks that govern protein conformational dynamics and structural responses to chemical or mechanical per...
M. Marfoglia, Miguel A. Pedraza-Joya, L. Guirardel et al.· PLoS Biology· 0 citations
The results indicate that the simplified energy landscape of multi-eGO limits the quantitative prediction of absolute kinetics while preserving thermodynamic information relevant to relative binding affinity, establishing multi-eGO as a computationally efficient approach for protein–peptide recognition and for predicti...
Camilla Ardizzone, Bruno Stegani, Fran Bačić Toplek et al.· bioRxiv· 0 citations
UniStab is introduced, an end-to-end framework for predicting stability changes across all mutation types by leveraging the implicit geometric reasoning of a pre-trained folding model and demonstrates state-of-the-art performance, particularly in the challenging scenarios of multi-point mutations and indels.
Hong Tan, Sheng-Geng Lin, Yi Xiong· Chemical Science· 0 citations
iSCALE serves as an effective in silico tool for large-scale protein-RNA binding ΔΔG prediction, which pushes the border of understanding in mutation-induced pathological outcomes.
This framework provides a clearer understanding of how methodological shifts have shaped the capabilities, limitations, and practical roles of recent models.
Wen-Gan He, Yong-Sheng Luo, Lihong Jiang et al.· 0 citations
Accurate prediction of mutation-induced protein stability responses, including changes in folding free energy and melting temperature, is critical for protein engineering. Existing models represent these related but non-equivalent measurements separately and often focus on single mutations. Here we present OmegaTherm,...
