RT Journal Article
SR Electronic
T1 US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.04.18.488565
DO 10.1101/2022.04.18.488565
A1 Chengxin Zhang
A1 Morgan Shine
A1 Anna Marie Pyle
A1 Yang Zhang
YR 2022
UL http://biorxiv.org/content/early/2022/04/18/2022.04.18.488565.abstract
AB Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules (proteins, RNAs, and DNAs). The pipeline is built on a uniform TM-score objective function coupled with a heuristic alignment searching algorithm. Large-scale benchmarks demonstrated significant advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the major advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search iterations, which significantly improve the accuracy and speed of the structural alignment process. Meanwhile, the universal protocol fusing different molecular and structural types helps facilitate the heterogeneous oligomer structure comparison and template-based protein-protein and protein-RNA/DNA docking.Competing Interest StatementThe authors have declared no competing interest.