PT  - JOURNAL ARTICLE
AU  - Chengxin Zhang
AU  - Morgan Shine
AU  - Anna Marie Pyle
AU  - Yang Zhang
TI  - US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes
AID  - 10.1101/2022.04.18.488565
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.04.18.488565
4099  - http://biorxiv.org/content/early/2022/04/18/2022.04.18.488565.short
4100  - http://biorxiv.org/content/early/2022/04/18/2022.04.18.488565.full
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.