US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes

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 consistent advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the main advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search…

• NS
  National Science Foundation

  Awards: MTM2025426, DBI2030790
• NH
  National Human Genome Research Institute

  Award: HG011868
• NI
  National Institute of General Medical Sciences

  Awards: OD026825, GM136422
• NI
  National Institute of Allergy and Infectious Diseases

  Award: AI134678