Ya-Ling Wu

HighFold4: extending AlphaFold3 to accurate cyclic peptide conformation prediction via custom chemical connectivity

Abstract While AlphaFold3 has revolutionized protein structure prediction and supports noncanonical amino acids, its architecture always fails to reliably generate the closed-ring topologies characteristic of cyclic peptides. Existing adaptations, such as imposing distance constraints via an offset matrix, enforce ring...