3 papers
eess.SP2025
GeoPep: A geometry-aware masked language model for protein-peptide binding site prediction
Dian Chen, Yunkai Chen, Tong Lin +2
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to pr…
q-bio.BM2025
State-aware protein-ligand complex prediction using AlphaFold3 with purified sequences
Enming Xing, Junjie Zhang, Shen Wang +1
Deep learning-based prediction of protein-ligand complexes has advanced significantly with the development of architectures such as AlphaFold3, Boltz-1, Chai-1, Protenix, and Neura…
q-bio.BM2025
Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2
Enming Xing, Junjie Zhang, Shen Wang +1
AlphaFold2 (AF2) has transformed protein structure prediction by harnessing co-evolutionary constraints embedded in multiple sequence alignments (MSAs). MSAs not only encode static…